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path: root/gn3/commands.py
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2023-04-06Remove deprecated `gn3.db_utils.database_connector` functionFrederick Muriuki Muriithi
Remove the deprecated function and fix a myriad of bugs that arise from removing the function. Issue: https://issues.genenetwork.org/issues/bugfix_coupling_current_app_and_db_utils
2022-12-21gn3: (gn3.random -> gn3.chancy): Rename module to avoid conflicts.Frederick Muriuki Muriithi
Rename the `gn3.random` module to gn3.chancy to avoid conflicts with Python's `random` module. * gn3/random.py -> gn3/chancy.py: rename module * gn3/commands.py: update import * gn3/computations/partial_correlations.py: update import * gn3/computations/qtlreaper.py: update import * gn3/computations/rust_correlation.py: update import * gn3/db/correlations.py: update import * gn3/db/traits.py: update import * gn3/heatmaps.py: update import * tests/integration/conftest.py: update import
2022-07-28Add command to run the sample correlations in an external processFrederick Muriuki Muriithi
2022-06-28Parse the method from UI before passing it to external processFrederick Muriuki Muriithi
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
2022-06-20Restrict partial correlation method choicesFrederick Muriuki Muriithi
- Have "Pearson's r" and "Spearman's rho" as the only valid choices for the partial correlations
2022-05-31Remove unnecessary statementFrederick Muriuki Muriithi
2022-05-24Run partial correlations with external scriptFrederick Muriuki Muriithi
Use new external script to run the partial correlations for both cases, i.e. - against an entire dataset, or - against selected traits
2022-05-21Fix linting errorsFrederick Muriuki Muriithi
2022-05-16Run computation in one-shot asynchronous processFrederick Muriuki Muriithi
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.
2022-03-11Fix some linting issuesFrederick Muriuki Muriithi
2022-03-08Fix tests, and issues caught by testsFrederick Muriuki Muriithi
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
2022-03-03Run partial correlations in an external processFrederick Muriuki Muriithi
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
2021-06-29Replace list with a tuple as an argument when setting success_codesBonfaceKilz
* 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".
2021-06-29gn3: commands: Add extra arg that sets the success codes to checkBonfaceKilz
* 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.
2021-06-25Check for the correct result codeBonfaceKilz
When programs terminate with an error, they usually return a -1!
2021-06-18Fix R/qtl command and the way keyword arguments are passedzsloan
2021-05-18Removed len from this if statement, since an empty list evaluates to False ↵zsloan
by itself
2021-05-18Account for boolean kwargs in compose_rqtl_cmdzsloan
2021-05-17Created compose_rqtl_command and generate_rqtl_command to create the actual ↵zsloan
command to be run from the command line; used the same pattern as for GEMMA for consistency
2021-03-10Queue the command only onceBonfaceKilz
2021-03-10Call Redis hset correctly in the right orderBonfaceKilz
2021-03-10Apply yapf file formatting to fileBonfaceKilz
2021-03-08bug: Put a space between gemma-wrapper argsBonfaceKilz
2021-03-08gn3: commands: Update docstringBonfaceKilz
2021-03-08Make the name of the redis job queue configurableBonfaceKilz
2021-02-24gn3: commands: Remove token and metadata_filename argsBonfaceKilz
2021-02-16Add extra option to set email when queueing CMDBonfaceKilz
The e-mail field will be used to send the results of the computation when it is completed.
2021-02-16gn3: commands: Add new procedure for running a commandBonfaceKilz
* gn3/commands.py (run_command): New procedure.
2021-02-12Add new procedure for queueing a commandBonfaceKilz
* gn3/commands.py (queue_cmd): New procedure. * tests/unit/test_commands.py: New test-cases for ^^.
2021-02-12Add new procedure for composing a gemma cmdBonfaceKilz
* gn3/commands.py: New file * tests/unit/test_commands.py: New test-cases for ^^.
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