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2023-09-05Remove unused importMunyoki Kilyungi
* tests/unit/test_file_utils.py: Delete gn3.cache_ipfs_file Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Delete IPFS testsMunyoki Kilyungi
* tests/unit/test_file_utils.py (test_cache_ipfs_file_cache_hit, test_cache_ipfs_file_cache_miss): Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2022-06-21tests: test_file_utils: Replace pytest.mark.skip with unittest.skipBonfaceKilz
"python setup.py test" won't skip "pytest.mark.skip" thereby leading to build failure when you try to package gn3.
2022-06-21test_file_utils: Disable test cases for "cache_ipfs_file"BonfaceKilz
* tests/unit/test_file_utils.py (test_cache_ipfs_file_cache_hit): Skip it. (test_cache_ipfs_file_cache_miss): Ditto.
2022-03-11Fix some linting issuesFrederick Muriuki Muriithi
2022-02-21Fix a myriad of linter issuesFrederick Muriuki Muriithi
* Use `with` in place of plain `open` * Use f-strings in place of `str.format()` * Remove string interpolation from queries - provide data as query parameters * other minor fixes
2022-02-17Use pytest's "mark" feature to categorise testsFrederick Muriuki Muriithi
Use pytest's `mark` feature to explicitly categorise the tests and run them per category
2021-05-13Rename file_utils to fs_helpersBonfaceKilz
Generally avoid naming things with a "utils" prefix/ suffix since it encourages contributors to dump any new functions there; and over time, as the code grows, things get messy...
2021-05-08Add extra genotype test fileBonfaceKilz
* tests/unit/test_data/genotype.txt: New file. * tests/unit/test_file_utils.py: Update failing test.
2021-03-23Convert Path object to a strBonfaceKilz
* gn3/file_utils.py (cache_ipfs_file): Return a str instead of a path object. * tests/unit/test_file_utils.py: Update failing tests.
2021-03-23Add function to cache ipfs filesBonfaceKilz
2021-03-23Apply autopep-8BonfaceKilz
2021-03-10Apply yapf file formatting to fileBonfaceKilz
2021-03-10Add extra tests for file utilsBonfaceKilz
In test server, files were not extracted properly. This test exposes the bug.
2021-03-10Run yapf-formatter against fileBonfaceKilz
2021-03-08Delete "lookup_file" procedureBonfaceKilz
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.
2021-02-16Add 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.
2021-02-12Use sorted list of files when calculating md5sums of directoryBonfaceKilz
* 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.
2021-02-12Add new procedure to return a python dict from a json fileBonfaceKilz
* gn3/file_utils.py (jsonfile_to_dict): New procedure * tests/unit/test_file_utils.py: New test-cases.
2021-02-12Add new procedure for looking up files in a given ENV variableBonfaceKilz
* gn3/file_utils.py (lookup_file): New function. * tests/unit/test_file_utils.py: New test cases for ^^.
2021-02-12Add function for computing the hash of a directoryBonfaceKilz
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