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2021-02-24Add new procedure that computes the hash of an array of stringsBonfaceKilz
2021-02-24Add mypy-typing to function...* gn3/computations/gemma.py (generate_random_n_string): Add typing to function. BonfaceKilz
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-wrapper...* guix.scm: New package propagated-input. * README.md: Mention that you require "guix-bioinformatics" package, because of the addition of "gemma-wrapper". BonfaceKilz
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 file...* 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. BonfaceKilz
2021-02-16Add extra option to set email when queueing CMD...The e-mail field will be used to send the results of the computation when it is completed. BonfaceKilz
2021-02-16Add python-bcrypt as a dependency...* guix.scm: Add python-bcrypt. * requirements.txt: Ditto. BonfaceKilz
2021-02-16Add basic integration tests to test out the APIBonfaceKilz
2021-02-16Register blueprints in gn3/app.py...* main.py: Move blueprint registrations to ... * gn3/app.py (create_app): ... here BonfaceKilz
2021-02-16Add instructions on how to run the flask appBonfaceKilz
2021-02-16Register gemma blueprintsBonfaceKilz
2021-02-16Add basic worker for processing commands...This will later be replaced with GNU Guile BonfaceKilz
2021-02-16Add new test cases for run_cmdBonfaceKilz
2021-02-16gn3: commands: Add new procedure for running a command...* gn3/commands.py (run_command): New procedure. BonfaceKilz
2021-02-15Add linting rules for any scm files. Useful for guix.scmBonfaceKilz
2021-02-15Update README with bootstrap instructions and how to run testsBonfaceKilz
2021-02-15Add genenetwork3 package definitionBonfaceKilz
2021-02-15requirements.txt: Add python-numpy 1.17.3BonfaceKilz
2021-02-15Add default redis configBonfaceKilz
2021-02-15Add test stubbed gemma endpointBonfaceKilz
2021-02-15Bootsrap the flask applicationBonfaceKilz
2021-02-12Add configuration file for the projectBonfaceKilz
2021-02-12Use sorted list of files when calculating md5sums of directory...* 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. BonfaceKilz
2021-02-12Create python-app.ymlBonfaceKilz
2021-02-12Add skeleton flask entry-pointBonfaceKilz
2021-02-12Add custom gn3 exceptionsBonfaceKilz
2021-02-12Add initial requirements.txt...Special care should be taken to make sure that this matches the version used in the packaged guix version of this project. BonfaceKilz
2021-02-12Add new procedure for queueing a command...* gn3/commands.py (queue_cmd): New procedure. * tests/unit/test_commands.py: New test-cases for ^^. BonfaceKilz
2021-02-12Add new procedure for composing a gemma cmd...* gn3/commands.py: New file * tests/unit/test_commands.py: New test-cases for ^^. BonfaceKilz
2021-02-12Add new procedure to return a python dict from a json file...* gn3/file_utils.py (jsonfile_to_dict): New procedure * tests/unit/test_file_utils.py: New test-cases. BonfaceKilz
2021-02-12Add new procedure for looking up files in a given ENV variable...* gn3/file_utils.py (lookup_file): New function. * tests/unit/test_file_utils.py: New test cases for ^^. BonfaceKilz
2021-02-12Add function for computing the hash of a directoryBonfaceKilz
2021-02-11Initial commitPjotr Prins
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