genenetwork3 - GeneNetwork3 REST API for data science and machine learning

Age	Commit message (Collapse)	Author
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

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	Create python-app.yml	BonfaceKilz

2021-02-12	Add skeleton flask entry-point	BonfaceKilz

2021-02-12	Add custom gn3 exceptions	BonfaceKilz

2021-02-12	Add initial requirements.txt	BonfaceKilz
	Special care should be taken to make sure that this matches the version used in the packaged guix version of this project.
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

2021-02-11	Initial commit	Pjotr Prins