Age | Commit message (Collapse) | Author | |
---|---|---|---|
2021-03-08 | Add 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. | |||
2021-03-08 | Create a more generic procedure for getting hash values of files | BonfaceKilz | |
* 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. | |||
2021-03-08 | 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 | BonfaceKilz | |
* gn3/api/general.py (upload_metadata): Update docstrings and update the use of "extract_uploaded_file" fn. | |||
2021-03-08 | Extract 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. | |||
2021-03-08 | Move "generate_random_n_string" to file_utils | BonfaceKilz | |
* gn3/computations/gemma.py (generaten_random_n_string): Move to... * gn3/file_utils.py: ... here. | |||
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 | BonfaceKilz | |
* gn3/computations/gemma.py (generate_random_n_string): Add typing to function. | |||
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 | |
2021-02-24 | gn3: api: gemma: Add endpoint for checking gemma-wrapper version | BonfaceKilz | |
2021-02-24 | gn3: commands: Remove token and metadata_filename args | BonfaceKilz | |
2021-02-24 | Add stubbed gemma endpoints | BonfaceKilz | |
2021-02-16 | Return the correct message and status code in "/metadata/upload" | BonfaceKilz | |
2021-02-16 | Register "general" blueprint endpoints | BonfaceKilz | |
2021-02-16 | Add extra default config for bcrypt | BonfaceKilz | |
2021-02-16 | Add new endpoint for uploading data | BonfaceKilz | |
2021-02-16 | Add procedure for uploading gzipped file | BonfaceKilz | |
* 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. | |||
2021-02-16 | Add extra option to set email when queueing CMD | BonfaceKilz | |
The e-mail field will be used to send the results of the computation when it is completed. | |||
2021-02-16 | Add basic integration tests to test out the API | BonfaceKilz | |
2021-02-16 | Register blueprints in gn3/app.py | BonfaceKilz | |
* main.py: Move blueprint registrations to ... * gn3/app.py (create_app): ... here | |||
2021-02-16 | gn3: commands: Add new procedure for running a command | BonfaceKilz | |
* gn3/commands.py (run_command): New procedure. | |||
2021-02-15 | Add default redis config | BonfaceKilz | |
2021-02-15 | Add test stubbed gemma endpoint | BonfaceKilz | |
2021-02-15 | Bootsrap the flask application | BonfaceKilz | |
2021-02-12 | Add configuration file for the project | BonfaceKilz | |
2021-02-12 | Use sorted list of files when calculating md5sums of directory | BonfaceKilz | |
* 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. | |||
2021-02-12 | Add custom gn3 exceptions | BonfaceKilz | |
2021-02-12 | Add new procedure for queueing a command | BonfaceKilz | |
* gn3/commands.py (queue_cmd): New procedure. * tests/unit/test_commands.py: New test-cases for ^^. | |||
2021-02-12 | Add new procedure for composing a gemma cmd | BonfaceKilz | |
* gn3/commands.py: New file * tests/unit/test_commands.py: New test-cases for ^^. | |||
2021-02-12 | Add new procedure to return a python dict from a json file | BonfaceKilz | |
* gn3/file_utils.py (jsonfile_to_dict): New procedure * tests/unit/test_file_utils.py: New test-cases. | |||
2021-02-12 | Add new procedure for looking up files in a given ENV variable | BonfaceKilz | |
* gn3/file_utils.py (lookup_file): New function. * tests/unit/test_file_utils.py: New test cases for ^^. | |||
2021-02-12 | Add function for computing the hash of a directory | BonfaceKilz | |