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-rw-r--r--tests/qc/test_cells.py20
-rw-r--r--tests/qc/test_cells_average.py2
-rw-r--r--tests/qc/test_cells_standard_error.py2
-rw-r--r--tests/qc/test_error_collection.py9
-rw-r--r--tests/qc/test_header.py25
-rw-r--r--tests/r_qtl/test_r_qtl2_qc.py19
6 files changed, 45 insertions, 32 deletions
diff --git a/tests/qc/test_cells.py b/tests/qc/test_cells.py
index e4a0959..937579f 100644
--- a/tests/qc/test_cells.py
+++ b/tests/qc/test_cells.py
@@ -22,12 +22,12 @@ def test_cell_value_errors_with_invalid_inputs2(num_str):
`quality_control.errors.InvalidValue` object which holds the error
information.
"""
- assert avg_invalid_value(0, 0, num_str) == InvalidValue(
- 0, 0, num_str, (
+ assert avg_invalid_value("test.file", 0, 0, num_str) == InvalidValue(
+ "test.file", 0, 0, num_str, (
f"Invalid value '{num_str}'. Expected string representing a number "
"with exactly three decimal places."))
- assert se_invalid_value(0, 0, num_str) == InvalidValue(
- 0, 0, num_str, (
+ assert se_invalid_value("test.file", 0, 0, num_str) == InvalidValue(
+ "test.file", 0, 0, num_str, (
f"Invalid value '{num_str}'. Expected string representing a number "
"with at least six decimal places."))
@@ -43,8 +43,8 @@ def test_cell_average_value_errors_if_not_three_decimal_places2(num_str):
object with the information about the placement of the invalid value.
"""
line, col = randint(0, 100), randint(0, 20)
- assert avg_invalid_value(line, col, num_str) == InvalidValue(
- line, col, num_str, (
+ assert avg_invalid_value("test.file", line, col, num_str) == InvalidValue(
+ "test.file", line, col, num_str, (
f"Invalid value '{num_str}'. Expected string representing a number "
"with exactly three decimal places."))
@@ -57,7 +57,7 @@ def test_cell_average_value_pass_if_three_decimal_places(num_str):
THEN: `avg_invalid_value` returns `None`
"""
line, col = randint(0, 100), randint(0, 20)
- assert avg_invalid_value(line, col, num_str) is None
+ assert avg_invalid_value("test.file", line, col, num_str) is None
@given(num_str=st.from_regex(r"^[0-9]+\.([0-9]{0,5}$)", fullmatch=True).filter(
lambda param: not re.match(r"^[0-9]+\.?0*$", param)))
@@ -70,8 +70,8 @@ def test_cell_standard_error_value_errors_if_less_than_six_decimal_places2(num_s
object with the information about the placement of the invalid value.
"""
line, col = randint(0, 100), randint(0, 20)
- assert se_invalid_value(line, col, num_str) == InvalidValue(
- line, col, num_str, (
+ assert se_invalid_value("test.file", line, col, num_str) == InvalidValue(
+ "test.file", line, col, num_str, (
f"Invalid value '{num_str}'. Expected string representing a number "
"with at least six decimal places."))
@@ -84,4 +84,4 @@ def test_cell_standard_error_value_pass_if_six_or_more_decimal_places(num_str):
THEN: `se_invalid_value` returns `None`
"""
line, col = randint(0, 100), randint(0, 20)
- assert se_invalid_value(line, col, num_str) is None
+ assert se_invalid_value("test.file", line, col, num_str) is None
diff --git a/tests/qc/test_cells_average.py b/tests/qc/test_cells_average.py
index 68fd4ec..b6ded31 100644
--- a/tests/qc/test_cells_average.py
+++ b/tests/qc/test_cells_average.py
@@ -14,4 +14,4 @@ def test_cell_average_value_pass_if_no_decimal_places(num_str):
THEN: `avg_invalid_value` returns `None`
"""
line, col = randint(0, 100), randint(0, 20)
- assert avg_invalid_value(line, col, num_str) is None
+ assert avg_invalid_value("test.file", line, col, num_str) is None
diff --git a/tests/qc/test_cells_standard_error.py b/tests/qc/test_cells_standard_error.py
index 90c13cf..fa9f1db 100644
--- a/tests/qc/test_cells_standard_error.py
+++ b/tests/qc/test_cells_standard_error.py
@@ -17,4 +17,4 @@ def test_cell_standard_error_value_errors_if_less_than_six_decimal_places2(num_s
THEN: `se_invalid_value` returns a `None`.
"""
line, col = randint(0, 100), randint(0, 20)
- assert invalid_value(line, col, num_str) is None
+ assert invalid_value("test.file", line, col, num_str) is None
diff --git a/tests/qc/test_error_collection.py b/tests/qc/test_error_collection.py
index 962d2c5..260fabf 100644
--- a/tests/qc/test_error_collection.py
+++ b/tests/qc/test_error_collection.py
@@ -44,11 +44,14 @@ def test_collect_errors(filepath, filetype, strains, count):
"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"),
+ "average_inconsistent_columns.tsv", 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"),
+ "average_inconsistent_columns.tsv", 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"))),))
+ "average_inconsistent_columns.tsv", 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
diff --git a/tests/qc/test_header.py b/tests/qc/test_header.py
index 5e54122..06647a2 100644
--- a/tests/qc/test_header.py
+++ b/tests/qc/test_header.py
@@ -11,17 +11,22 @@ from quality_control.headers import (
@given(headers=st.lists(st.text(max_size=10), max_size=1))
def test_invalid_header_with_list_of_one_value(headers):
"""Test `invalid_header` with invalid header row"""
- assert invalid_header(0, headers) == InvalidValue(
- 0, 0, "<TAB>".join(headers),
+ assert invalid_header("test.file", 0, headers) == InvalidValue(
+ "test.file", 0, 0, "<TAB>".join(headers),
"The header MUST contain at least 2 columns")
@pytest.mark.unit_test
@given(headings=st.lists(st.text(min_size=2, max_size=10), min_size=2))
def test_invalid_headings_with_invalid_inputs(headings):
"Verify that the check for header validity works"
- assert invalid_headings(0, ("BXD1", "BXD2", "BXD3"), headings) == tuple(
- InvalidValue(0, col, heading, f"'{heading}' not a valid strain.")
- for col, heading in enumerate(headings, start=2))
+ assert invalid_headings(
+ "test.file", 0, ("BXD1", "BXD2", "BXD3"), headings) == tuple(
+ InvalidValue("test.file",
+ 0,
+ col,
+ heading,
+ f"'{heading}' not a valid strain.")
+ for col, heading in enumerate(headings, start=2))
@pytest.mark.unit_test
@pytest.mark.parametrize(
@@ -30,7 +35,7 @@ def test_invalid_headings_with_invalid_inputs(headings):
(("Individual", "AStrain", "AnotherStrain", "YetAnotherStrain"))])
def test_invalid_header_with_valid_headers(headers):
"Verify that the check for header validity works"
- assert invalid_header(0, headers) is None
+ assert invalid_header("test.file", 0, headers) is None
@pytest.mark.unit_test
@pytest.mark.parametrize(
@@ -40,7 +45,7 @@ def test_invalid_header_with_valid_headers(headers):
("AStrain", "AnotherStrain", "YetAnotherStrain"))])
def test_invalid_headings_with_valid_headings(strains, headings):
"Verify that the check for header validity works"
- assert invalid_headings(0, strains, headings) == tuple()
+ assert invalid_headings("test.file", 0, strains, headings) == tuple()
@pytest.mark.unit_test
@pytest.mark.parametrize(
@@ -50,8 +55,8 @@ def test_invalid_headings_with_valid_headings(strains, headings):
"AStrain"), {"AStrain": (2, 5)})])
def test_duplicate_headers_with_repeated_column_headings(headers, repeated):
"""Check that parsing fails if any header is duplicated"""
- assert duplicate_headings(0, headers) == tuple(
- DuplicateHeading(0, cols, head, (
+ assert duplicate_headings("test.file", 0, headers) == tuple(
+ DuplicateHeading("test.file", 0, cols, head, (
f"Heading '{head}', is repeated in columns "
f"{','.join(str(i) for i in cols)}"))
for head, cols in repeated.items())
@@ -63,4 +68,4 @@ def test_duplicate_headers_with_repeated_column_headings(headers, repeated):
(("Individual", "AStrain", "AnotherStrain", "YetAnotherStrain",))])
def test_duplicate_headers_with_unique_column_headings(headers):
"""Check that parsing fails if any header is duplicated"""
- assert duplicate_headings(0, headers) == tuple()
+ assert duplicate_headings("test.file", 0, headers) == tuple()
diff --git a/tests/r_qtl/test_r_qtl2_qc.py b/tests/r_qtl/test_r_qtl2_qc.py
index d12172e..05db30e 100644
--- a/tests/r_qtl/test_r_qtl2_qc.py
+++ b/tests/r_qtl/test_r_qtl2_qc.py
@@ -124,9 +124,12 @@ def test_missing_files(filepath, expected):
("tests/r_qtl/test_files/test_geno.zip",
tuple()),
("tests/r_qtl/test_files/geno_with_missing_genotypes.zip",
- (InvalidValue(1, "AXR-1", "X", "Invalid value 'X'. Expected one of ('L', 'C')."),
- InvalidValue(2, "EC.480C", "Y", "Invalid value 'Y'. Expected one of ('L', 'C')."),
- InvalidValue(6, "HH.335C-Col/PhyA", "H", f"Invalid value 'H'. Expected one of ('L', 'C').")))))
+ (InvalidValue("geno", 1, "AXR-1", "X",
+ "Invalid value 'X'. Expected one of ('L', 'C')."),
+ InvalidValue("geno", 2, "EC.480C",
+ "Y", "Invalid value 'Y'. Expected one of ('L', 'C')."),
+ InvalidValue("geno", 6, "HH.335C-Col/PhyA", "H",
+ f"Invalid value 'H'. Expected one of ('L', 'C').")))))
def test_geno_errors(filepath, expected):
"""
GIVEN: A R/qtl2 bundle
@@ -145,10 +148,12 @@ def test_geno_errors(filepath, expected):
("tests/r_qtl/test_files/pheno_without_errors.zip",
tuple()),
("tests/r_qtl/test_files/pheno_with_errors.zip",
- (InvalidValue(1, "liver", "61.92", ("Invalid value '61.92'. Expected numerical value "
- "with at least 3 decimal places.")),
- InvalidValue(2, "spleen", "brrr", ("Invalid value 'brrr'. Expected numerical value "
- "with at least 3 decimal places."))))))
+ (InvalidValue("pheno", 1, "liver", "61.92", (
+ "Invalid value '61.92'. Expected numerical value "
+ "with at least 3 decimal places.")),
+ InvalidValue("pheno", 2, "spleen", "brrr", (
+ "Invalid value 'brrr'. Expected numerical value "
+ "with at least 3 decimal places."))))))
def test_pheno_errors(filepath, expected):
"""
GIVEN: A R/qtl2 bundle
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 09:00:45 +0000