| Age | Commit message (Expand) | Author |
|---|
| 2022-12-23 | Help: Provide some help content for end user | Frederick Muriuki Muriithi |
| 2022-11-16 | ui: provide error messaging if file is not selected. | Frederick Muriuki Muriithi |
| 2022-11-16 | ui: Don't show upload progress indicator if file is not selected. | 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 |
| 2022-09-08 | 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 |
| 2022-08-31 | Commit missing files. | 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 | 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 | 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 | 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 | Fix linting and typing errors | 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 |
| 2022-06-21 | Test the progress indication feature | 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 |
| 2022-06-17 | Test endpoint '/parse/parse'...* Ensure error messages are displayed if a request is made to the
'/parse/parse' endpoint with invalid, or missing data.
| Frederick Muriuki Muriithi |
| 2022-06-15 | Fix linting and type errors | Frederick Muriuki Muriithi |
| 2022-06-15 | Setup test fixtures and initial tests for web-UI | Frederick Muriuki Muriithi |
| 2022-06-13 | Add upload progress indicator | 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 | Expire the jobs in 14 days by default | 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 |
| 2022-05-27 | Remove unnecessary print statement | Frederick Muriuki Muriithi |
| 2022-05-20 | Use standard-error rather than standard_error for consistency...The CLI scripts use "standard-error" so update the web version to fit
in with that.
| Frederick Muriuki Muriithi |
| 2022-05-20 | Fix minor bugs | Frederick Muriuki Muriithi |
| 2022-05-20 | Handle errors...Implement code to handle errors in the processing of files.
| 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 |
| 2022-05-02 | Optimise strain names parsing...- Use a way faster way of parsing the strains file
| Frederick Muriuki Muriithi |
| 2022-04-28 | Use sqlite3 to save the jobs metadata...* Use sqlite to save the jobs metadata and enable UI update of the
progress for large files
| Frederick Muriuki Muriithi |
| 2022-04-28 | Update queuing and display results of file parsing...* Make the 'worker' functions free from needing the application
context by passing all the details they need as arguments.
* Enable the display of parsing results.
| Frederick Muriuki Muriithi |
