genenetwork3 - GeneNetwork3 REST API for data science and machine learning

Age	Commit message (Collapse)	Author
2022-04-01	Run python-black in file	BonfaceKilz
	* gn3/csvcmp.py: Run "black -l 79 ..." * tests/unit/db/test_sample_data.py: Ditto. * tests/unit/test_csvcmp.py: Ditto.
2022-03-18	Clean all csv fields before diffing	BonfaceKilz
	There was a subtle bug where "csvdiff" generated an error related to "different column headings" caused something akin to diffing: "a, b \n, ..." with "a, b\n, ...". * gn3/csvcmp.py (csv_diff): Clean csv texts before any diffing. * tests/unit/test_csvcmp.py (test_csv_diff_same_columns): Modify test case to capture aforementioned bug.
2022-03-18	Create new function for cleaning individual fields in csv text	BonfaceKilz
	* gn3/csvcmp.py (clean_csv_text): New function. * tests/unit/test_csvcmp.py: Import "csv_text". (test_clean_csv_text): Test case for the above.
2022-03-14	Only loop through the diff's modifications if it exists	BonfaceKilz

2022-03-14	Given a csv text and permissible headers, extract invalid headers	BonfaceKilz
	* gn3/csvcmp.py (extract_invalid_csv_headers): New function. * tests/unit/test_csvcmp.py: Import "extract_invalid_csv_headers". (test_extract_invalid_csv_headers_with_some_wrong_headers): Test case for the above.
2022-03-14	Get all permissible column data	BonfaceKilz
	* gn3/csvcmp.py: Import "Any" and "List". (get_allowable_sampledata_headers): New function. * tests/unit/test_csvcmp: Import "get_allowable_sampledata_headers". (test_get_allowable_csv_headers): Test case for the above.
2022-03-12	Fix mypy issues	BonfaceKilz

2022-03-12	Fix pylint issues	BonfaceKilz

2022-03-12	Compose csv-diff command within single quotes	BonfaceKilz
	* gn3/csvcmp.py (csv_diff): Use single quotes. There was a change in 6d39c92 that broke this.
2022-03-12	Delete noisy "print" statement	BonfaceKilz

2022-03-12	Fill in empty values in csv text with: "x"	BonfaceKilz
	* gn3/csvcmp.py (fill_csv): Update this function to allow empty lists to be filled with the default value(set in the args). * tests/unit/test_csvcmp.py (test_fill_csv): Update test to capture above.
2022-03-12	Extract a strain name given a csv string and it's header	BonfaceKilz
	* gn3/csvcmp.py (extract_strain_name): New function. * gn3/db/sample_data (delete_sample_data): Use the aforementioned function. (insert_sample_data): Ditto. * tests/unit/test_csvcmp: Test cases for above.
2022-03-12	Don't add extra key "Column" to dict if there are no changes	BonfaceKilz
	gn3/csvcmp.py (csv_diff): If the diff is empty, don't add an extra key "Column" to the dictionary. tests/unit/test_csvcmp (test_csv_diff_only_column_change): Add test-case for the above.
2022-03-12	Fill CSV text if there are non-even rows	BonfaceKilz
	Should you try to run `csvdiff` against 2 csv files with either file having a non-even columns, there will be an error. As such, the csv files need to be "filled" before running `csvdiff`. * gn3/csvcmp (csv_diff): For non-even rows in the csv files, fill the csv rows.
2022-03-12	Create new method for filling csv with a default value	BonfaceKilz
	* gn3/csvcmp.py (fill_csv): Given a csv text with uneven or incomplete fields whole length are less than width, fill them with a value which defaults to "x". * tests/unit/test_csvcmp.py (test_fill_csv): Test cases for the above.
2022-03-12	Replace "all" with "and"	BonfaceKilz
	* gn3/csvcmp.py (remove_insignificant_edits): "all" evaluates all elements and throws an error if when `abs(float(x) - float(y)) < epsilon` is processed. Use "and" instead because of it's short-circuiting behaviour.
2022-03-12	Store columns in the output dict	BonfaceKilz
	When inserting, deleting, or editing case-attributes, we need the column headers in order to be able to know identify the attribute of interest. * gn3/csvcmp.py (csv_diff): Add extra "Column" key in returned dict.
2022-03-12	Add methods for working with csv data	BonfaceKilz
	gn3/csvcmp.py: New file (create_dirs_if_not_exists): From a list of dirs, create them if they don't exist. (remove_insignificant_edits): Given a dict with a "Modification" key, remove edits with "delta < ε". (csv_diff): Generate a csv_diff using the "csvdiff" tool packaged in guix. tests/unit/test_csvcmp.py: Add some tests for "gn3/csvcmp.py"