| Age | Commit message (Expand) | Author |
|---|
| 2024-01-09 | WIP: Install genotypes from R/qtl2 bundle...Load the genotype information from the R/qtl2 bundle and insert it
into the database.
| Frederick Muriuki Muriithi |
| 2024-01-09 | Fix linting errors | Frederick Muriuki Muriithi |
| 2024-01-09 | scripts: Log to redis...Add a logger that will log output to a redis list. This will be useful
to retrieve the output(s) of the running script to help display some
form of progress to the user.
| Frederick Muriuki Muriithi |
| 2024-01-08 | Use extracted functions and fix bugs | 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 |
| 2023-12-18 | 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 |
| 2023-11-30 | 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 | Implement data insertion...- Hook up external data insertion script to webserver code
- Provide rudimentary status indication
- Generalise some job creation details
| Frederick Muriuki Muriithi |
| 2022-08-04 | Handle stderr output...* Fix bug where stderr was not being updated on redis appropriately
| 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 |
| 2022-07-19 | Check connections before launching...* qc_app/__init__.py (refactor): Check connection before launching the
application
* qc_app/check_connections.py (new file): Add code to check
connections
* qc_app/db_utils.py (refactor): enable passing the database uri as an
argument to the connection creation function.
* scripts/worker.py (refactor): Use new code to check for redis
connection.
| Frederick Muriuki Muriithi |
| 2022-07-19 | Add generic worker script...Add a generic worker script, whose purpose is:
- to launch the specific worker script
- to capture both stdin and stderr streams and put them on redis
In this way, we can launch redis-aware and redis-unaware workers and
capture their outputs or errors for later processing.
| Frederick Muriuki Muriithi |
| 2022-07-19 | Rename file validation script...As preparation for building a new generic worker script, this commit
renames the file validation script from 'worker.py' to
'validate_file.py' so as to ensure the name conforms better to what
the script does.
| Frederick Muriuki Muriithi |
| 2022-07-07 | Replace 'magic' with builtin 'mimetypes'...Use the builtin mimetypes which gives better results
| Frederick Muriuki Muriithi |
| 2022-06-28 | Check for inconsistent columns...The number columns in each contents line should be equal to the nember
of columns in the header line.
| Frederick Muriuki Muriithi |
| 2022-06-15 | Fix linting and type errors | Frederick Muriuki Muriithi |
| 2022-06-10 | Enable upload of zipfiles | Frederick Muriuki Muriithi |
| 2022-06-02 | Enable user abortion of file parsing...Enable the user to abort the background parsing of the file.
| Frederick Muriuki Muriithi |
| 2022-06-02 | Add an error display to the progress status report...Enable the progress status page to show all the errors found at any
point during the processing of the file.
| Frederick Muriuki Muriithi |
| 2022-05-19 | Update Web-UI: use new error collection paradigm...- README.org: document how to run scripts manually
- manifest.scm: remove python-rq as a dependency
- qc_app/jobs.py: rework job launching and processing
- qc_app/parse.py: use reworked job processing
- qc_app/templates/job_progress.html: display progress correctly
- qc_app/templates/parse_results.html: display final results
- scripts/worker.py: new worker script
| Frederick Muriuki Muriithi |
| 2022-05-19 | Extract progress indication from the parsing...Since progress indication is not part of the parsing, this commit
extracts the progress indication into functions with well defined
input arguments that hide the progress indication logic from the
parsing function.
| Frederick Muriuki Muriithi |
| 2022-05-18 | Update CLI: use new error collection code...Use the new code that collects the errors in the CLI client.
| Frederick Muriuki Muriithi |
| 2022-05-11 | Tag string as a python f-string to fix error display bug | Frederick Muriuki Muriithi |
| 2022-05-02 | Optimise strain names parsing...- Use a way faster way of parsing the strains file
| Frederick Muriuki Muriithi |
| 2022-04-27 | Enable managing app via setup.py...While the application is developed with GNU Guix, the end user might
not be using it, and therefore, this commit provides a way for the
user to install the application with the usual python package
management systems.
| Frederick Muriuki Muriithi |
