| Age | Commit message (Expand) | Author |
|---|
| 2021-03-10 | Rename "covariates" to "covars" in endpoints for consistency | BonfaceKilz |
| 2021-03-10 | Queue the command only once | BonfaceKilz |
| 2021-03-10 | Fix k-compute command when "loco" is true | BonfaceKilz |
| 2021-03-10 | Call Redis hset correctly in the right order | BonfaceKilz |
| 2021-03-10 | Apply yapf file formatting to file | BonfaceKilz |
| 2021-03-10 | Add extra endpoint for when TOKEN isn't provided | BonfaceKilz |
| 2021-03-10 | Extract file to the correct location | BonfaceKilz |
| 2021-03-08 | Remove unused imports | BonfaceKilz |
| 2021-03-08 | Delete "generate_gemma_computation_cmd" | BonfaceKilz |
| 2021-03-08 | Remove "/k-gwa-computation" | BonfaceKilz |
| 2021-03-08 | Add "/k-gwa-compute/covars/loco/<chromosomes>/maf/<maf>/<token>"•••Reviewed-by: BonfaceKilz <me@bonfacemunyoki.com>
| BonfaceKilz |
| 2021-03-08 | Add "/gemma/k-gwa-compute/loco/<chromosomes>/maf/<maf>/<token>" | BonfaceKilz |
| 2021-03-08 | Add "/k-gwa-compute/covars/<token>" | BonfaceKilz |
| 2021-03-08 | Add "/gemma/k-gwa-compute/<token>" | BonfaceKilz |
| 2021-03-08 | Replace "compute_k_values" with "generate_gemma_cmd" | BonfaceKilz |
| 2021-03-08 | Use new "compute_k_values" procedure | BonfaceKilz |
| 2021-03-08 | Add generic fn for computing k and gwa values | BonfaceKilz |
| 2021-03-08 | Apply pep-8 formatting•••Began using elpy's format code fn
| BonfaceKilz |
| 2021-03-08 | Add new endpoint•••"/gwa-compute/<k_filename>/loco/covariates/maf/<maf>/<token>"
| BonfaceKilz |
| 2021-03-08 | Replace "generate_gemma_computation_cmd" with "compose_gemma_cmd" | BonfaceKilz |
| 2021-03-08 | bug: Put a space between gemma-wrapper args | BonfaceKilz |
| 2021-03-08 | Add new endpoint: "/gwa-compute/<k_filename>/loco/maf/<maf>/<token>" | BonfaceKilz |
| 2021-03-08 | Add new endpoint: "/gwa-compute/covars/<k_filename>/<token>" | BonfaceKilz |
| 2021-03-08 | Add new endpoint: "/gwa-compute/<k_filename>/<token>" | BonfaceKilz |
| 2021-03-08 | Add new endpoint: "/gemma/k-compute/loco/<chromosomes>/<token>" | BonfaceKilz |
| 2021-03-08 | Prepend all endpoints with "api" | BonfaceKilz |
| 2021-03-08 | Add new endpoint: "/gemma/k-compute/<token>"•••* gn3/api/gemma.py (compute_k): New function.
* tests/integration/test_gemma.py (tesk_k_compute): New test case.
| BonfaceKilz |
| 2021-03-08 | Create a more generic procedure for getting hash values of files•••* gn3/file_utils.py (get_hash_of_values): New procedure.
(get_dir_hash): Use more generic "get_hash_of_values" to compute the hash of a
directory.
| BonfaceKilz |
| 2021-03-08 | Replace APP_DEFAULTS dict with actual conf params | BonfaceKilz |
| 2021-03-08 | Delete "lookup_file" procedure | BonfaceKilz |
| 2021-03-08 | Use new extract_uploaded_file fn when uploading metadata•••* gn3/api/general.py (upload_metadata): Update docstrings and update the use
of "extract_uploaded_file" fn.
| BonfaceKilz |
| 2021-03-08 | Extract files to "/TMPDIR/TOKEN"•••TOKEN is the user token
* gn3/file_utils.py (extract_uploaded_file): Add extra param "token". If a
token is empty, create a new directory based off that token.
* tests/unit/test_file_utils.py: Update failing tests.
| BonfaceKilz |
| 2021-03-08 | Move "generate_random_n_string" to file_utils•••* gn3/computations/gemma.py (generaten_random_n_string): Move to...
* gn3/file_utils.py: ... here.
| BonfaceKilz |
| 2021-03-08 | Fix failing tests | BonfaceKilz |
| 2021-03-08 | gn3: commands: Update docstring | BonfaceKilz |
| 2021-03-08 | Add extra endpoint for checking the status of a command | BonfaceKilz |
| 2021-03-08 | Make the name of the redis job queue configurable | BonfaceKilz |
| 2021-02-24 | Rename "/gemma/run" to "/gemma/k-gwa-computation" | BonfaceKilz |
| 2021-02-24 | Update how gemma(extracted from gn2) is computed | BonfaceKilz |
| 2021-02-24 | Create a new helper function for generating k_values and GWA | BonfaceKilz |
| 2021-02-24 | Add procedure that checks whether a list of paths exist | BonfaceKilz |
| 2021-02-24 | Check if phenotype exists before creating one | BonfaceKilz |
| 2021-02-24 | Add new procedure that computes the hash of an array of strings | BonfaceKilz |
| 2021-02-24 | Add mypy-typing to function•••* gn3/computations/gemma.py (generate_random_n_string): Add typing to function.
| BonfaceKilz |
| 2021-02-24 | Append random 6 chars to generated phenotype file | BonfaceKilz |
| 2021-02-24 | Create a new method for generating a valid phenotype file on the fly | BonfaceKilz |
| 2021-02-24 | Add GENODIR extra param | BonfaceKilz |
| 2021-02-24 | Add endpoint for running GEMMA | BonfaceKilz |
| 2021-02-24 | Delete unnececessary gemma endpoints | BonfaceKilz |
| 2021-02-24 | Remove test "/gemma" stub | BonfaceKilz |
