Remove obsoleted code. Fix linting errors.

Remove the old code that relied on exceptions to parse errors in the
uploaded files.

1 files changed, 10 insertions, 32 deletions

diff --git a/tests/qc/test_error_collection.py b/tests/qc/test_error_collection.py
index 466f455..fe85bb1 100644
--- a/tests/qc/test_error_collection.py
+++ b/tests/qc/test_error_collection.py
@@ -1,33 +1,9 @@
+"""Check that error collection works as expected"""
+
 import pytest
 
-from quality_control.parsing import take, FileType, parse_errors
-from quality_control.parsing import collect_errors
-
-@pytest.mark.slow
-@pytest.mark.parametrize(
-    "filepath,filetype,seek_pos",
-    (("tests/test_data/average_crlf.tsv", FileType.AVERAGE, 0),
-     ("tests/test_data/average_error_at_end_200MB.tsv", FileType.AVERAGE,
-      205500004 # Skip first 500K lines
-      ),
-     ("tests/test_data/average.tsv", FileType.AVERAGE, 0),
-     ("tests/test_data/standarderror_1_error_at_end.tsv",
-      FileType.STANDARD_ERROR, 0),
-     ("tests/test_data/standarderror.tsv", FileType.STANDARD_ERROR, 0),
-     ("tests/test_data/duplicated_headers_no_data_errors.tsv",
-      FileType.AVERAGE, 0)))
-def test_parse_errors(filepath, filetype, strains, seek_pos):
-    """
-    Check that only errors are returned, and that certain properties hold for
-    said errors.
-    """
-    for error in parse_errors(filepath, filetype, strains, seek_pos):
-        assert isinstance(error, dict)
-        assert "filepath" in error
-        assert "filetype" in error
-        assert "position" in error
-        assert "error" in error and isinstance(error["error"], str)
-        assert "message" in error
+from quality_control.errors import InvalidValue, DuplicateHeading
+from quality_control.parsing import take, FileType, collect_errors
 
 @pytest.mark.parametrize(
     "sample,num,expected",
@@ -35,13 +11,11 @@ def test_parse_errors(filepath, filetype, strains, seek_pos):
      ([0, 1, 2, 3], 200, [0, 1, 2, 3]),
      (("he", "is", "a", "lovely", "boy"), 3, ["he", "is", "a"])))
 def test_take(sample, num, expected):
+    """Check that `take` works correctly."""
     taken = take(sample, num)
     assert len(taken) <= num
     assert taken == expected
 
-
-## ==================================================
-
 @pytest.mark.slow
 @pytest.mark.parametrize(
     "filepath,filetype,count",
@@ -55,4 +29,8 @@ def test_take(sample, num, expected):
      ("tests/test_data/duplicated_headers_no_data_errors.tsv",
       FileType.AVERAGE, 10)))
 def test_collect_errors(filepath, filetype, strains, count):
-    assert len(collect_errors(filepath, filetype, strains, count)) <= count
+    """Check that `collect_errors` works as expected."""
+    results = take(collect_errors(filepath, filetype, strains), count)
+    def __valid_instance(item):
+        return isinstance(item, (InvalidValue, DuplicateHeading))
+    assert all(__valid_instance(error) for error in results)