| Age | Commit message (Expand) | Author |
|---|---|---|
| 2022-06-28 | Parse the method from UI before passing it to external process...To reduce the chances of the system failing due to the external process being launched with the wrong parameters, add a parsing stage that converts the method from the UI into a form acceptable by the CLI script. * gn3/commands.py: parse the method from UI * scripts/partial_correlations.py: simplify the acceptable methods | Frederick Muriuki Muriithi |
| 2022-06-20 | Restrict partial correlation method choices...- Have "Pearson's r" and "Spearman's rho" as the only valid choices for the partial correlations | Frederick Muriuki Muriithi |
| 2022-05-31 | Remove unnecessary statement | Frederick Muriuki Muriithi |
| 2022-05-24 | Run partial correlations with external script...Use new external script to run the partial correlations for both cases, i.e. - against an entire dataset, or - against selected traits | Frederick Muriuki Muriithi |
| 2022-05-21 | Fix linting errors | Frederick Muriuki Muriithi |
| 2022-05-16 | Run computation in one-shot asynchronous process...After reworking the worker/runner to have a one-shot mode, add a function that queues up the task and then runs the worker in the one-shot mode to process the computation in the background. | Frederick Muriuki Muriithi |
| 2022-03-11 | Fix some linting issues | Frederick Muriuki Muriithi |
| 2022-03-08 | Fix tests, and issues caught by tests...Fix some issues caught by tests due to changes introducing the hand-off of the partial correlations computations to an external process Fix some issues due to the changes that introduce context managers for database connections Update some tests to take the above two changes into consideration | Frederick Muriuki Muriithi |
| 2022-03-03 | Run partial correlations in an external process...Run the partial correlations code in an external python process decoupling it from the server and making it asynchronous. Summary of changes: * gn3/api/correlation.py: - Remove response processing code - Queue partial corrs processing - Create new endpoint to get results * gn3/commands.py - Compose the pcorrs command to be run in an external process - Enable running of subprocess commands with list args * gn3/responses/__init__.py: new module indicator file * gn3/responses/pcorrs_responses.py: Hold response processing code extracted from ~gn3.api.correlations.py~ file * scripts/partial_correlations.py: CLI script to process the pcorrs * sheepdog/worker.py: - Add the *genenetwork3* path at the beginning of the ~sys.path~ list to override any GN3 in the site-packages - Add any environment variables to be set for the command to be run | Frederick Muriuki Muriithi |
| 2021-06-29 | Replace list with a tuple as an argument when setting success_codes...* gn3/commands.py (run_cmd): Replace type of success_codes from List to Tuple * gn3/computations/diff.py (generate_diff): Pass success_codes as a Tuple when calling "run_cmd". | BonfaceKilz |
| 2021-06-29 | gn3: commands: Add extra arg that sets the success codes to check...* gn3/commands.py (run_cmd): Some commands like "diff" return non-standard error codes. To make this fn more robust, add an extra optional argument that sets what successful codes to check. | BonfaceKilz |
| 2021-06-25 | Check for the correct result code...When programs terminate with an error, they usually return a -1! | BonfaceKilz |
| 2021-06-18 | Fix R/qtl command and the way keyword arguments are passed | zsloan |
| 2021-05-18 | Removed len from this if statement, since an empty list evaluates to False by... | zsloan |
| 2021-05-18 | Account for boolean kwargs in compose_rqtl_cmd | zsloan |
| 2021-05-17 | Created compose_rqtl_command and generate_rqtl_command to create the actual c... | zsloan |
| 2021-03-10 | Queue the command only once | BonfaceKilz |
| 2021-03-10 | Call Redis hset correctly in the right order | BonfaceKilz |
| 2021-03-10 | Apply yapf file formatting to file | BonfaceKilz |
| 2021-03-08 | bug: Put a space between gemma-wrapper args | BonfaceKilz |
| 2021-03-08 | gn3: commands: Update docstring | BonfaceKilz |
| 2021-03-08 | Make the name of the redis job queue configurable | BonfaceKilz |
| 2021-02-24 | gn3: commands: Remove token and metadata_filename args | BonfaceKilz |
| 2021-02-16 | Add extra option to set email when queueing CMD...The e-mail field will be used to send the results of the computation when it is completed. | BonfaceKilz |
| 2021-02-16 | gn3: commands: Add new procedure for running a command...* gn3/commands.py (run_command): New procedure. | BonfaceKilz |
| 2021-02-12 | Add new procedure for queueing a command...* gn3/commands.py (queue_cmd): New procedure. * tests/unit/test_commands.py: New test-cases for ^^. | BonfaceKilz |
| 2021-02-12 | Add new procedure for composing a gemma cmd...* gn3/commands.py: New file * tests/unit/test_commands.py: New test-cases for ^^. | BonfaceKilz |
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