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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-pink 1.4.1 (git 2.36.1) at 2025-10-06 15:26:49 +0000