| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2022-06-17 | Add configs for pytest | 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 |
| 2022-06-16 | Add more UI tests...- Test upload with missing or invalid data
- Test triggering the parsing of the file
| 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 |
| 2022-06-10 | Update tests: Accept zeroes as valid values | 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 |
| 2022-06-02 | Provide missing argument | Frederick Muriuki Muriithi |
| 2022-05-27 | Update documentation | Frederick Muriuki Muriithi |
| 2022-05-27 | Remove unnecessary print statement | Frederick Muriuki Muriithi |
| 2022-05-27 | Accept zeroes | Frederick Muriuki Muriithi |
| 2022-05-27 | Revert "Accept exponential notation for standard-error files"...This reverts commit 960c1a5b831d8761a3e1716f86ded4cc5b67eea0.
After meeting with Arthur, it was confirmed that the CSV file should
not have values in the exponential notation.
| Frederick Muriuki Muriithi |
| 2022-05-20 | Accept exponential notation for standard-error files | 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 |
| 2022-05-19 | 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 |
| 2022-05-18 | Remove obsoleted code. Fix linting errors....Remove the old code that relied on exceptions to parse errors in the
uploaded files.
| Frederick Muriuki Muriithi |
