Track filename in the errors

R/qtl2 bundles can contain more than one file, of the same type. When
errors are encountered in any of the files, we need to be able to
inform the user which file it is, in addition to the line and column
number.

6 files changed, 55 insertions, 42 deletions

diff --git a/quality_control/average.py b/quality_control/average.py
index ad732d0..bf288de 100644
--- a/quality_control/average.py
+++ b/quality_control/average.py
@@ -4,12 +4,13 @@ from typing import Union
 from .utils import cell_error
 from .errors import InvalidValue
 
-def invalid_value(line_number: int, column_number: int, val: str) -> Union[
-        InvalidValue, None]:
+def invalid_value(
+        filename: str, line_number: int, column_number: int, val: str) -> Union[
+            InvalidValue, None]:
     """Return an `InvalidValue` object if `val` is not a valid "averages"
     value."""
     return cell_error(
-        r"^([0-9]+\.[0-9]{3}|[0-9]+\.?0*)$", val, line=line_number,
+        r"^([0-9]+\.[0-9]{3}|[0-9]+\.?0*)$", val, filename=filename, line=line_number,
         column=column_number, value=val, message=(
             f"Invalid value '{val}'. "
             "Expected string representing a number with exactly three "
diff --git a/quality_control/checks.py b/quality_control/checks.py
index 475eb9e..bdfd12b 100644
--- a/quality_control/checks.py
+++ b/quality_control/checks.py
@@ -52,7 +52,8 @@ def decimal_places_pattern(mini: int, maxi: Optional[int] = None) -> re.Pattern:
         + r")$"
     )
 
-def decimal_points_error(lineno: int,
+def decimal_points_error(filename: str,# pylint: disable=[too-many-arguments]
+                         lineno: int,
                          field: str,
                          value: str,
                          mini: int,
@@ -61,7 +62,7 @@ def decimal_points_error(lineno: int,
     Check that 'value' in a decimal number with the appropriate decimal places.
     """
     if not bool(decimal_places_pattern(mini, maxi).match(value)):
-        return InvalidValue(lineno, field, value, (
+        return InvalidValue(filename, lineno, field, value, (
             f"Invalid value '{value}'. Expected numerical value " +
             f"with at least {mini} decimal places" +
             (f" and at most {maxi} decimal places" if maxi is not None else "")
diff --git a/quality_control/errors.py b/quality_control/errors.py
index fff6c7c..01afa81 100644
--- a/quality_control/errors.py
+++ b/quality_control/errors.py
@@ -3,10 +3,10 @@
 from collections import namedtuple
 
 InvalidValue = namedtuple(
-    "InvalidValue", ("line", "column", "value", "message"))
+    "InvalidValue", ("filename", "line", "column", "value", "message"))
 
 DuplicateHeading = namedtuple(
-    "DuplicateHeading", ("line", "columns", "heading", "message"))
+    "DuplicateHeading", ("filename", "line", "columns", "heading", "message"))
 
 InconsistentColumns = namedtuple(
-    "InconsistentColumns", ("line", "header_count", "contents_count", "message"))
+    "InconsistentColumns", ("filename", "line", "header_count", "contents_count", "message"))
diff --git a/quality_control/headers.py b/quality_control/headers.py
index f4f4dad..436ea5a 100644
--- a/quality_control/headers.py
+++ b/quality_control/headers.py
@@ -5,30 +5,34 @@ from typing import Union, Tuple, Sequence
 
 from quality_control.errors import InvalidValue, DuplicateHeading
 
-def invalid_header(
-        line_number: int, headers: Sequence[str]) -> Union[InvalidValue, None]:
+def invalid_header(filename: str,
+                   line_number: int,
+                   headers: Sequence[str]) -> Union[InvalidValue, None]:
     """Return an `InvalidValue` object if the header row has less than 2
     items."""
     if len(headers) < 2:
         return InvalidValue(
-            line_number, 0, "<TAB>".join(headers),
+            filename, line_number, 0, "<TAB>".join(headers),
             "The header MUST contain at least 2 columns")
     return None
 
 def invalid_headings(
-        line_number: int, strains: Sequence[str],
+        filename: str, line_number: int, strains: Sequence[str],
         headings: Sequence[str]) -> Union[Tuple[InvalidValue, ...], None]:
     """Return tuple of `InvalidValue` objects for each error found for every
     column heading."""
     return tuple(
-        InvalidValue(
-            line_number, col, header, f"'{header}' not a valid strain.")
+        InvalidValue(filename,
+                     line_number,
+                     col,
+                     header,
+                     f"'{header}' not a valid strain.")
         for col, header in
         enumerate(headings, start=2) if header not in strains)
 
-def duplicate_headings(
-        line_number: int,
-        headers: Sequence[str]) -> Tuple[DuplicateHeading, ...]:
+def duplicate_headings(filename: str,
+                       line_number: int,
+                       headers: Sequence[str]) -> Tuple[DuplicateHeading, ...]:
     """Return a tuple of `DuplicateHeading` objects for each column heading that
     is a duplicate of another column heading."""
     def __update_columns__(acc, item):
@@ -42,7 +46,7 @@ def duplicate_headings(
     }
     return tuple(
         DuplicateHeading(
-            line_number, columns, heading, (
+            filename, line_number, columns, heading, (
                 f"Heading '{heading}', is repeated in columns "
                 f"{','.join(str(i) for i in columns)}"))
         for heading, columns in repeated.items())
diff --git a/quality_control/parsing.py b/quality_control/parsing.py
index f7a664f..f1d21fc 100644
--- a/quality_control/parsing.py
+++ b/quality_control/parsing.py
@@ -1,6 +1,7 @@
 """Module handling the high-level parsing of the files"""
 import collections
 from enum import Enum
+from pathlib import Path
 from functools import partial
 from typing import Tuple, Union, Generator, Callable, Optional
 
@@ -30,44 +31,44 @@ def strain_names(dbconn: mdb.Connection, speciesid: int) -> tuple[str, ...]:
             lambda item: bool(item.strip() if item is not None else item),
             (name for names in samplenames for name in names))))
 
-def header_errors(line_number, fields, strains):
+def header_errors(filename, line_number, fields, strains):
     """Gather all header row errors."""
     return (
-        (invalid_header(line_number, fields),) +
-        invalid_headings(line_number, strains, fields[1:]) +
-        duplicate_headings(line_number, fields))
+        (invalid_header(filename, line_number, fields),) +
+        invalid_headings(filename, line_number, strains, fields[1:]) +
+        duplicate_headings(filename, line_number, fields))
 
-def empty_value(line_number, column_number, value):
+def empty_value(filename, line_number, column_number, value):
     """Check for empty field values."""
     if value == "":
-        return InvalidValue(
-            line_number, column_number, value, "Empty value for column")
+        return InvalidValue(filename, line_number, column_number, value,
+                            "Empty value for column")
     return None
 
-def average_errors(line_number, fields):
+def average_errors(filename, line_number, fields):
     """Gather all errors for a line in a averages file."""
     return (
-        (empty_value(line_number, 1, fields[0]),) +
+        (empty_value(filename, line_number, 1, fields[0]),) +
         tuple(
-            avg.invalid_value(line_number, *field)
+            avg.invalid_value(filename, line_number, *field)
             for field in enumerate(fields[1:], start=2)))
 
-def se_errors(line_number, fields):
+def se_errors(filename, line_number, fields):
     """Gather all errors for a line in a standard-errors file."""
     return (
-        (empty_value(line_number, 1, fields[0]),) +
+        (empty_value(filename, line_number, 1, fields[0]),) +
         tuple(
-            se.invalid_value(line_number, *field)
+            se.invalid_value(filename, line_number, *field)
             for field in enumerate(fields[1:], start=2)))
 
-def make_column_consistency_checker(header_row):
+def make_column_consistency_checker(filename, header_row):
     """Build function to check for column consistency"""
     headers = tuple(field.strip() for field in header_row.split("\t"))
     def __checker__(line_number, contents_row):
         contents = tuple(field.strip() for field in contents_row.split("\t"))
         if len(contents) != len(headers):
             return InconsistentColumns(
-                line_number, len(headers), len(contents),
+                filename, line_number, len(headers), len(contents),
                 (f"Header row has {len(headers)} columns while row "
                  f"{line_number} has {len(contents)} columns"))
         return None
@@ -79,8 +80,10 @@ def collect_errors(
         user_aborted: Callable = lambda: False) -> Generator:
     """Run checks against file and collect all the errors"""
     errors:Tuple[Union[InvalidValue, DuplicateHeading], ...] = tuple()
-    def __process_errors__(line_number, line, error_checker_fn, errors = tuple()):
+    def __process_errors__(
+            filename, line_number, line, error_checker_fn, errors = tuple()):
         errs = error_checker_fn(
+            filename,
             line_number,
             tuple(field.strip() for field in line.split("\t")))
         if errs is None:
@@ -90,6 +93,7 @@ def collect_errors(
         return errors + (errs,)
 
     with open_file(filepath) as input_file:
+        filename = Path(filepath).name
         for line_number, line in enumerate(input_file, start=1):
             if user_aborted():
                 break
@@ -98,9 +102,11 @@ def collect_errors(
                 line = line.decode("utf-8")
 
             if line_number == 1:
-                consistent_columns_checker = make_column_consistency_checker(line)
+                consistent_columns_checker = make_column_consistency_checker(
+                    filename, line)
                 for error in __process_errors__(
-                        line_number, line, partial(header_errors, strains=strains),
+                        filename, line_number, line,
+                        partial(header_errors, strains=strains),
                         errors):
                     yield error
 
@@ -110,7 +116,7 @@ def collect_errors(
                     yield col_consistency_error
 
                 for error in __process_errors__(
-                        line_number, line, (
+                        filename, line_number, line, (
                             average_errors if filetype == FileType.AVERAGE
                             else se_errors),
                         errors):
diff --git a/quality_control/standard_error.py b/quality_control/standard_error.py
index 90beb8a..00b1ac6 100644
--- a/quality_control/standard_error.py
+++ b/quality_control/standard_error.py
@@ -4,17 +4,18 @@ from typing import Union
 from .utils import cell_error
 from .errors import InvalidValue
 
-def invalid_value(
-        line_number: int, column_number: int, val: str) -> Union[
-            InvalidValue, None]:
+def invalid_value(filename: str,
+                  line_number: int,
+                  column_number: int,
+                  val: str) -> Union[InvalidValue, None]:
     """
     Returns a `quality_control.errors.InvalidValue` object in the case where
     `val` is not a valid input for standard error files, otherwise, it returns
     `None`.
     """
     return cell_error(
-        r"^([0-9]+\.[0-9]{6,}|[0-9]+\.?0*)$", val, line=line_number,
-        column=column_number, value=val, message=(
+        r"^([0-9]+\.[0-9]{6,}|[0-9]+\.?0*)$", val, filename=filename,
+        line=line_number, column=column_number, value=val, message=(
             f"Invalid value '{val}'. "
             "Expected string representing a number with at least six "
             "decimal places."))