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2021-03-10Update test to ensure redis.hset is called correctlyBonfaceKilz
2021-03-10Apply yapf file formatting to fileBonfaceKilz
2021-03-10Add extra tests for file utilsBonfaceKilz
In test server, files were not extracted properly. This test exposes the bug.
2021-03-10Run yapf-formatter against fileBonfaceKilz
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>"BonfaceKilz
Reviewed-by: BonfaceKilz <me@bonfacemunyoki.com>
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
2021-03-08Add generic fn for computing k and gwa valuesBonfaceKilz
2021-03-08Apply pep-8 formattingBonfaceKilz
Began using elpy's format code fn
2021-03-08Add new endpointBonfaceKilz
"/gwa-compute/<k_filename>/loco/covariates/maf/<maf>/<token>"
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>"BonfaceKilz
* gn3/api/gemma.py (compute_k): New function. * tests/integration/test_gemma.py (tesk_k_compute): New test case.
2021-03-08Replace APP_DEFAULTS dict with actual conf paramsBonfaceKilz
2021-03-08Delete "lookup_file" procedureBonfaceKilz
2021-03-08Add test data directoryBonfaceKilz
2021-03-08Update failing tests.BonfaceKilz
2021-03-08Extract files to "/TMPDIR/TOKEN"BonfaceKilz
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.
2021-03-08Fix failing testsBonfaceKilz
2021-03-08Add dummy test data filesBonfaceKilz
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
2021-02-24Add tests for "/gemma/run" endpointBonfaceKilz
2021-02-24Create a new helper function for generating k_values and GWABonfaceKilz
2021-02-24Add new procedure that computes the hash of an array of stringsBonfaceKilz
2021-02-24Create a new method for generating a valid phenotype file on the flyBonfaceKilz
2021-02-24Add integration test for "/gemma/version" endpointBonfaceKilz
2021-02-24Update "compose_gemma_cmd" testsBonfaceKilz
2021-02-16Add test cases for "/metadata/upload" endpointBonfaceKilz
2021-02-16Add procedure for uploading gzipped fileBonfaceKilz
* 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.
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.
2021-02-16Add basic integration tests to test out the APIBonfaceKilz
2021-02-16Add new test cases for run_cmdBonfaceKilz
2021-02-12Use sorted list of files when calculating md5sums of directoryBonfaceKilz
* gn3/file_utils.py (get_dir_hash): Sort list of files before calculating their md5sums. * tests/unit/test_file_utils.py (test_get_dir_hash): Update test-case md5sum.
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 ^^.
2021-02-12Add new procedure to return a python dict from a json fileBonfaceKilz
* gn3/file_utils.py (jsonfile_to_dict): New procedure * tests/unit/test_file_utils.py: New test-cases.
2021-02-12Add new procedure for looking up files in a given ENV variableBonfaceKilz
* gn3/file_utils.py (lookup_file): New function. * tests/unit/test_file_utils.py: New test cases for ^^.
2021-02-12Add function for computing the hash of a directoryBonfaceKilz
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 16:29:11 +0000