genenetwork3 - GeneNetwork3 REST API for data science and machine learning

Age	Commit message (Collapse)	Author
2022-05-06	Fix linting and typing errors	Frederick Muriuki Muriithi

2022-04-29	Replace whole header with the longest one, instead of just the	zsloan
	non-CaseAttribute headers (before this caused issues if someone was adding case attributes to a file that already contained some case attributes)
2022-04-29	Get max string length instead when comparing headers	zsloan
	Apparently max(string1, string2) in Python gets the strong that is highest alphabetically, but I'm pretty sure this line was intenteded to get the header with the most items (which this commit doesn't fully address; you could still end up with a situation where some case attributes were removed while others were added, though that should be rare)
2022-04-12	Delete "get_allowable_sampledata_headers"	BonfaceKilz
	* gn3/csvcmp.py (get_allowable_sampledata_headers): Delete it. * tests/unit/test_csvcmp.py: Remove "get_allowable_sampledata_headers" import. (test_get_allowable_csv_headers): Delete it.
2022-04-07	Fix mypy error	BonfaceKilz

2022-04-07	Add method for parsing a csv header from uploaded sample-data file	BonfaceKilz
	* gn3/csvcmp.py (parse_csv_column): New function. * tests/unit/test_csvcmp.py: Test case for the above.
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"