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authorFrederick Muriuki Muriithi2022-06-28 15:20:54 +0300
committerFrederick Muriuki Muriithi2022-06-28 15:20:54 +0300
commite68c807e6598a4087d7c83510ba33c81139f5544 (patch)
tree1c8d52c686e64cf8751f51d85bf8164ff8b9653c /tests
parent3eef6d582245c80e274c9e135028de90788a712b (diff)
downloadgn-uploader-e68c807e6598a4087d7c83510ba33c81139f5544.tar.gz
Check for inconsistent columns
The number columns in each contents line should be equal to the nember of columns in the header line.
Diffstat (limited to 'tests')
-rw-r--r--tests/qc/test_error_collection.py20
1 files changed, 19 insertions, 1 deletions
diff --git a/tests/qc/test_error_collection.py b/tests/qc/test_error_collection.py
index fe85bb1..ee1e6c2 100644
--- a/tests/qc/test_error_collection.py
+++ b/tests/qc/test_error_collection.py
@@ -2,8 +2,9 @@
import pytest
-from quality_control.errors import InvalidValue, DuplicateHeading
from quality_control.parsing import take, FileType, collect_errors
+from quality_control.errors import (
+ InvalidValue, DuplicateHeading, InconsistentColumns)
@pytest.mark.parametrize(
"sample,num,expected",
@@ -34,3 +35,20 @@ def test_collect_errors(filepath, filetype, strains, count):
def __valid_instance(item):
return isinstance(item, (InvalidValue, DuplicateHeading))
assert all(__valid_instance(error) for error in results)
+
+@pytest.mark.parametrize(
+ "filepath,filetype,expected",
+ (("tests/test_data/average_inconsistent_columns.tsv", FileType.AVERAGE,
+ (InconsistentColumns(
+ 4, 4, 5, "Header row has 4 columns while row 4 has 5 columns"),
+ InconsistentColumns(
+ 5, 4, 3, "Header row has 4 columns while row 5 has 3 columns"),
+ InconsistentColumns(
+ 6, 4, 7, "Header row has 4 columns while row 6 has 7 columns"))),))
+def test_collect_inconsistent_column_errors(filepath, filetype, strains, expected):
+ """
+ Given: A file with inconsistent columns in certain lines
+ When: collect_errors is run on the file
+ Then: All the lines with inconsistent columns are flagged
+ """
+ assert tuple(collect_errors(filepath, filetype, strains)) == expected