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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.
2021-03-08Create a more generic procedure for getting hash values of filesBonfaceKilz
* 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.
2021-03-08Replace APP_DEFAULTS dict with actual conf paramsBonfaceKilz
2021-03-08Delete "lookup_file" procedureBonfaceKilz
2021-03-08Add test data directoryBonfaceKilz
2021-03-08Ignore similarities in imports section when lintingBonfaceKilz
2021-03-08Update failing tests.BonfaceKilz
2021-03-08Use new extract_uploaded_file fn when uploading metadataBonfaceKilz
* gn3/api/general.py (upload_metadata): Update docstrings and update the use of "extract_uploaded_file" fn.
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.
2021-03-08Move "generate_random_n_string" to file_utilsBonfaceKilz
* gn3/computations/gemma.py (generaten_random_n_string): Move to... * gn3/file_utils.py: ... here.
2021-03-08Fix failing testsBonfaceKilz
2021-03-08Add dummy test data filesBonfaceKilz
2021-03-08Add basic gemma documentation on how to use it from gn3BonfaceKilz
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
2021-03-08guix.scm: Add jupyter depsBonfaceKilz
2021-02-24Rename "/gemma/run" to "/gemma/k-gwa-computation"BonfaceKilz
2021-02-24Add tests for "/gemma/run" endpointBonfaceKilz
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 functionBonfaceKilz
* gn3/computations/gemma.py (generate_random_n_string): Add typing to function.
2021-02-24Gitignore generated windows/ mac filesBonfaceKilz
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
2021-02-24Add integration test for "/gemma/version" endpointBonfaceKilz
2021-02-24gn3: api: gemma: Add endpoint for checking gemma-wrapper versionBonfaceKilz
2021-02-24Update "compose_gemma_cmd" testsBonfaceKilz
2021-02-24gn3: commands: Remove token and metadata_filename argsBonfaceKilz
2021-02-24Add type checking to gh workflowsBonfaceKilz
2021-02-24Add stubbed gemma endpointsBonfaceKilz
2021-02-17Add gemma-wrapperBonfaceKilz
* guix.scm: New package propagated-input. * README.md: Mention that you require "guix-bioinformatics" package, because of the addition of "gemma-wrapper".
2021-02-16Add test cases for "/metadata/upload" endpointBonfaceKilz
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 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 python-bcrypt as a dependencyBonfaceKilz
* guix.scm: Add python-bcrypt. * requirements.txt: Ditto.
2021-02-16Add basic integration tests to test out the APIBonfaceKilz
2021-02-16Register blueprints in gn3/app.pyBonfaceKilz
* main.py: Move blueprint registrations to ... * gn3/app.py (create_app): ... here
2021-02-16Add instructions on how to run the flask appBonfaceKilz
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