| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 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 | Add dummy test data files | BonfaceKilz | |
| 2021-03-08 | Add basic gemma documentation on how to use it from gn3 | 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 | |
| 2021-03-08 | guix.scm: Add jupyter deps | BonfaceKilz | |
| 2021-02-24 | Rename "/gemma/run" to "/gemma/k-gwa-computation" | BonfaceKilz | |
| 2021-02-24 | Add tests for "/gemma/run" endpoint | 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 | Gitignore generated windows/ mac files | 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 | |
| 2021-02-24 | Add integration test for "/gemma/version" endpoint | BonfaceKilz | |
| 2021-02-24 | gn3: api: gemma: Add endpoint for checking gemma-wrapper version | BonfaceKilz | |
| 2021-02-24 | Update "compose_gemma_cmd" tests | BonfaceKilz | |
| 2021-02-24 | gn3: commands: Remove token and metadata_filename args | BonfaceKilz | |
| 2021-02-24 | Add type checking to gh workflows | BonfaceKilz | |
| 2021-02-24 | Add stubbed gemma endpoints | BonfaceKilz | |
| 2021-02-17 | Add gemma-wrapper | BonfaceKilz | |
| * guix.scm: New package propagated-input. * README.md: Mention that you require "guix-bioinformatics" package, because of the addition of "gemma-wrapper". | |||
| 2021-02-16 | Add test cases for "/metadata/upload" endpoint | 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 python-bcrypt as a dependency | BonfaceKilz | |
| * guix.scm: Add python-bcrypt. * requirements.txt: Ditto. | |||
| 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 | Add instructions on how to run the flask app | BonfaceKilz | |
| 2021-02-16 | Register gemma blueprints | BonfaceKilz | |
| 2021-02-16 | Add basic worker for processing commands | BonfaceKilz | |
| This will later be replaced with GNU Guile | |||
| 2021-02-16 | Add new test cases for run_cmd | BonfaceKilz | |
| 2021-02-16 | gn3: commands: Add new procedure for running a command | BonfaceKilz | |
| * gn3/commands.py (run_command): New procedure. | |||
| 2021-02-15 | Add linting rules for any scm files. Useful for guix.scm | BonfaceKilz | |
| 2021-02-15 | Update README with bootstrap instructions and how to run tests | BonfaceKilz | |
| 2021-02-15 | Add genenetwork3 package definition | BonfaceKilz | |
| 2021-02-15 | requirements.txt: Add python-numpy 1.17.3 | BonfaceKilz | |
 |
index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
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