aboutsummaryrefslogtreecommitdiff
path: root/gn3
AgeCommit message (Expand)Author
2021-03-08Delete "generate_gemma_computation_cmd"BonfaceKilz
2021-03-08Remove "/k-gwa-computation"BonfaceKilz
2021-03-08Add "/k-gwa-compute/covars/loco/<chromosomes>/maf/<maf>/<token>"...Reviewed-by: BonfaceKilz <me@bonfacemunyoki.com> BonfaceKilz
2021-03-08Add "/gemma/k-gwa-compute/loco/<chromosomes>/maf/<maf>/<token>"BonfaceKilz
2021-03-08Add "/k-gwa-compute/covars/<token>"BonfaceKilz
2021-03-08Add "/gemma/k-gwa-compute/<token>"BonfaceKilz
2021-03-08Replace "compute_k_values" with "generate_gemma_cmd"BonfaceKilz
2021-03-08Use new "compute_k_values" procedureBonfaceKilz
2021-03-08Add generic fn for computing k and gwa valuesBonfaceKilz
2021-03-08Apply pep-8 formatting...Began using elpy's format code fn BonfaceKilz
2021-03-08Add new endpoint..."/gwa-compute/<k_filename>/loco/covariates/maf/<maf>/<token>" BonfaceKilz
2021-03-08Replace "generate_gemma_computation_cmd" with "compose_gemma_cmd"BonfaceKilz
2021-03-08bug: Put a space between gemma-wrapper argsBonfaceKilz
2021-03-08Add new endpoint: "/gwa-compute/<k_filename>/loco/maf/<maf>/<token>"BonfaceKilz
2021-03-08Add new endpoint: "/gwa-compute/covars/<k_filename>/<token>"BonfaceKilz
2021-03-08Add new endpoint: "/gwa-compute/<k_filename>/<token>"BonfaceKilz
2021-03-08Add new endpoint: "/gemma/k-compute/loco/<chromosomes>/<token>"BonfaceKilz
2021-03-08Prepend all endpoints with "api"BonfaceKilz
2021-03-08Add 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
2021-03-08Create 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
2021-03-08Replace APP_DEFAULTS dict with actual conf paramsBonfaceKilz
2021-03-08Delete "lookup_file" procedureBonfaceKilz
2021-03-08Use 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
2021-03-08Extract 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
2021-03-08Move "generate_random_n_string" to file_utils...* gn3/computations/gemma.py (generaten_random_n_string): Move to... * gn3/file_utils.py: ... here. BonfaceKilz
2021-03-08Fix failing testsBonfaceKilz
2021-03-08gn3: commands: Update docstringBonfaceKilz
2021-03-08Add extra endpoint for checking the status of a commandBonfaceKilz
2021-03-08Make the name of the redis job queue configurableBonfaceKilz
2021-02-24Rename "/gemma/run" to "/gemma/k-gwa-computation"BonfaceKilz
2021-02-24Update how gemma(extracted from gn2) is computedBonfaceKilz
2021-02-24Create a new helper function for generating k_values and GWABonfaceKilz
2021-02-24Add procedure that checks whether a list of paths existBonfaceKilz
2021-02-24Check if phenotype exists before creating oneBonfaceKilz
2021-02-24Add new procedure that computes the hash of an array of stringsBonfaceKilz
2021-02-24Add mypy-typing to function...* gn3/computations/gemma.py (generate_random_n_string): Add typing to function. BonfaceKilz
2021-02-24Append random 6 chars to generated phenotype fileBonfaceKilz
2021-02-24Create a new method for generating a valid phenotype file on the flyBonfaceKilz
2021-02-24Add GENODIR extra paramBonfaceKilz
2021-02-24Add endpoint for running GEMMABonfaceKilz
2021-02-24Delete unnececessary gemma endpointsBonfaceKilz
2021-02-24Remove test "/gemma" stubBonfaceKilz
2021-02-24gn3: api: gemma: Add endpoint for checking gemma-wrapper versionBonfaceKilz
2021-02-24gn3: commands: Remove token and metadata_filename argsBonfaceKilz
2021-02-24Add stubbed gemma endpointsBonfaceKilz
2021-02-16Return the correct message and status code in "/metadata/upload"BonfaceKilz
2021-02-16Register "general" blueprint endpointsBonfaceKilz
2021-02-16Add extra default config for bcryptBonfaceKilz
2021-02-16Add new endpoint for uploading dataBonfaceKilz
2021-02-16Add procedure for uploading gzipped file...* gn3/file_utils.py (extract_uploaded_file): New procedure. * tests/unit/test_file_utils.py: Test cases for ^^. * tests/unit/upload-data.tar.gz: New test data. BonfaceKilz
generated by cgit v1.2.3 (git 2.46.2) at 2024-12-04 09:17:15 +0000