diff options
| -rw-r--r-- | gn3/data_helpers.py | 13 | ||||
| -rw-r--r-- | tests/unit/test_data_helpers.py | 26 |
2 files changed, 37 insertions, 2 deletions
diff --git a/gn3/data_helpers.py b/gn3/data_helpers.py index f0d971e..741a885 100644 --- a/gn3/data_helpers.py +++ b/gn3/data_helpers.py @@ -5,7 +5,7 @@ data structures. from math import ceil from functools import reduce -from typing import Any, Tuple, Sequence +from typing import Any, Tuple, Sequence, Optional def partition_all(num: int, items: Sequence[Any]) -> Tuple[Tuple[Any, ...], ...]: """ @@ -23,3 +23,14 @@ def partition_all(num: int, items: Sequence[Any]) -> Tuple[Tuple[Any, ...], ...] tuple(items[start:stop]) for start, stop # type: ignore[has-type] in reduce( __compute_start_stop__, iterations, tuple())]) + +def parse_csv_line( + line:str, delimiter: str = ",", quoting:Optional[str] = '"') -> Tuple[str, ...]: + """ + Parses a line from a CSV file into a tuple of strings. + + This is a migration of the `web.webqtl.utility.webqtlUtil.readLineCSV` + function in GeneNetwork1. + """ + return tuple( + col.strip("{} \t\n".format(quoting)) for col in line.split(delimiter)) diff --git a/tests/unit/test_data_helpers.py b/tests/unit/test_data_helpers.py index 1eec3cc..39aea45 100644 --- a/tests/unit/test_data_helpers.py +++ b/tests/unit/test_data_helpers.py @@ -4,7 +4,7 @@ Test functions in gn3.data_helpers from unittest import TestCase -from gn3.data_helpers import partition_all +from gn3.data_helpers import partition_all, parse_csv_line class TestDataHelpers(TestCase): """ @@ -35,3 +35,27 @@ class TestDataHelpers(TestCase): ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9), ))): with self.subTest(n=count, items=items): self.assertEqual(partition_all(count, items), expected) + + def test_parse_csv_line(self): + """ + Test parsing a single line from a CSV file + + Given: + - `line`: a line read from a csv file + - `delimiter`: the expected delimiter in the csv file + - `quoting`: the quoting enclosing each column in the csv file + When: + - `line` is parsed with the `parse_csv_file` with the given + parameters + Then: + - return a tuple of the columns in the CSV file, without the + delimiter and quoting + """ + for line, delimiter, quoting, expected in ( + ('"this","is","a","test"', ",", '"', ("this", "is", "a", "test")), + ('"this","is","a","test"', ",", None, ('"this"', '"is"', '"a"', '"test"'))): + with self.subTest(line=line, delimiter=delimiter, quoting=quoting): + self.assertEqual( + parse_csv_line( + line=line, delimiter=delimiter, quoting=quoting), + expected) |