| Age | Commit message (Expand) | Author |
|---|
| 2022-11-16 | qc: Allow whole numbers or numbers where the decimals are all zeroes | Frederick Muriuki Muriithi |
| 2022-11-16 | ui: Only display the "alert-success" green on completion...* To avoid confusion, only display the "alert-success" green on
completion of the parsing process. While parsing, if there are no
errors, then display the "No errors found so far" message without
the green colour.
| Frederick Muriuki Muriithi |
| 2022-11-12 | Accept plain text (text/plain) files | Frederick Muriuki Muriithi |
| 2022-09-16 | Add redis and mariadb as propagated inputs | Frederick Muriuki Muriithi |
| 2022-09-16 | Deactivate tests | Frederick Muriuki Muriithi |
| 2022-09-16 | Config: Add apache2 sample config file | Frederick Muriuki Muriithi |
| 2022-09-16 | Add dependency: gunicorn...* guix.scm: Add dependency (gunicorn)
| Frederick Muriuki Muriithi |
| 2022-09-08 | Use sys.executable and setup default environment...Use the sys.executable to get the correct python binary to run the
external processes, and setup the environment to point to the correct
PYTHONPATH.
| Frederick Muriuki Muriithi |
| 2022-09-08 | Update dependencies...* guix.scm: reorganise the dependencies
* setup.cfg: change the `install_requires` values
| Frederick Muriuki Muriithi |
| 2022-08-31 | Commit missing files. | Frederick Muriuki Muriithi |
| 2022-08-31 | Update test: use new script name. | Frederick Muriuki Muriithi |
| 2022-08-31 | Provide database port where relevant. | Frederick Muriuki Muriithi |
| 2022-08-31 | Check connections outside app factory...Check the connections in the wsgi.py file, outside of the `create_app`
application factory to avoid issues with tests failing due to test app
not initialising because of missing connections in the test
environment.
| 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 |
| 2022-08-04 | Fix typo: 'species' -> 'speciesid' | Frederick Muriuki Muriithi |
| 2022-08-04 | UX: Enable selecting radio by clicking anywhere on the row...Ease the selection of a radio button by allowing the user to click on
any of the table cells that are in the same row as the radio button of
concern.
| 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 | Rework: Use generic worker script to launch process...Use the generic worker script as the interface for launching external
processes.
| 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 |
| 2022-07-19 | Implement confirmation stage...Provide user with a confirmation stage where they can verify all the
data before inserting into the database.
| Frederick Muriuki Muriithi |
| 2022-07-19 | Enable creation of new dataset...Enable the user to create a new dataset should the need arise.
A few extra fixes were done, such as:
- Provide list of average methods to choose from
- Provide input elements for some expected fields
- Add a new confirmation step before doing the actual data update
| Frederick Muriuki Muriithi |
| 2022-07-19 | Replace redirect with user confirmation...Rather than using the redirect, that led to exposing the study id as a
get parameter, this commit adds an auxilliary step that allows the
user to choose whether to continue with the new study or go back and
select an existing study.
| Frederick Muriuki Muriithi |
| 2022-07-19 | Implement dataset selection...- Implement UI enabling selection from existing datasets
- Start implementation of UI that enables creation of new dataset
| Frederick Muriuki Muriithi |
| 2022-07-19 | Implement study creation...Enable the creation of the new study, and redirect appropriately with
the new study id.
| Frederick Muriuki Muriithi |
| 2022-07-19 | Fix macro | Frederick Muriuki Muriithi |
| 2022-07-19 | Add missing db_utils module | Frederick Muriuki Muriithi |
| 2022-07-19 | Add 'group' and 'tissue' selection....- Build code to populate the "Group" and "Tissue" dropdown lists
- Enable redirect with POST data (code 307) in case there is input
error to enable the user fix their errors
- Move hidden fields to macro to reduce repetition
| Frederick Muriuki Muriithi |
| 2022-07-19 | Implement select study...Implement the select study UI
| Frederick Muriuki Muriithi |
| 2022-07-19 | Select the platform (GeneChipId) first | Frederick Muriuki Muriithi |
| 2022-07-07 | Rework guix.scm to use latest commit...Rather than specifying a specific commit in the development guix.scm
this commit has the system automatically get the latest commit and use
that for building the package object.
| Frederick Muriuki Muriithi |
| 2022-07-07 | Fix linting and typing errors | Frederick Muriuki Muriithi |
| 2022-07-07 | Fix test | Frederick Muriuki Muriithi |
| 2022-07-07 | Replace 'magic' with builtin 'mimetypes'...Use the builtin mimetypes which gives better results
| Frederick Muriuki Muriithi |
| 2022-07-07 | Rework styling for form elements | Frederick Muriuki Muriithi |
| 2022-07-07 | Add filetype details to database update code...The filetype determines the queries to be run to update the database,
therefore, this commit adds filetype information.
| Frederick Muriuki Muriithi |
| 2022-07-07 | Provide selection for GeneChips...The GeneChipId value is required for the data being inserted, so this
commit provides the UI to enable selection of the chip.
| Frederick Muriuki Muriithi |
| 2022-07-06 | Implement UI for dataset selection...As part of updating the database with the new data, there is a need to
select the appropriate dataset that the data belongs to, and this
commit provides the UI to assist the user do that.
| 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 |
| 2022-06-22 | Test zipfiles uploads: commit forgotten tests | Frederick Muriuki Muriithi |
| 2022-06-22 | Test the results pages | Frederick Muriuki Muriithi |
| 2022-06-21 | Test the progress indication feature | Frederick Muriuki Muriithi |
| 2022-06-21 | Rename fixture: fixture gives back the redis url, not a server | Frederick Muriuki Muriithi |
| 2022-06-21 | Update tests: Ensure errors return status code 400 | Frederick Muriuki Muriithi |
| 2022-06-21 | Test the upload of zip files works as expected...- Ensure errors respond with status code 400
- Ensure error messages are displayed for any invalid zip file that is
uploaded.
| Frederick Muriuki Muriithi |
