From 1b61b59dcc8e92cbeaedfa7183df281555ba2828 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 8 Feb 2024 04:00:20 +0300
Subject: Use error objects rather than plain tuple values.

---
 r_qtl/fileerrors.py           |  5 +++++
 r_qtl/r_qtl2_qc.py            | 24 ++++++++++++++----------
 tests/r_qtl/test_r_qtl2_qc.py | 21 ++++++++++++---------
 3 files changed, 31 insertions(+), 19 deletions(-)
 create mode 100644 r_qtl/fileerrors.py

diff --git a/r_qtl/fileerrors.py b/r_qtl/fileerrors.py
new file mode 100644
index 0000000..e76676c
--- /dev/null
+++ b/r_qtl/fileerrors.py
@@ -0,0 +1,5 @@
+"""QC errors as distinguished from actual exceptions"""
+from collections import namedtuple
+
+MissingFile = namedtuple(
+    "MissingFile", ("controlfilekey", "filename", "message"))
diff --git a/r_qtl/r_qtl2_qc.py b/r_qtl/r_qtl2_qc.py
index b45c17a..8d4fc19 100644
--- a/r_qtl/r_qtl2_qc.py
+++ b/r_qtl/r_qtl2_qc.py
@@ -2,11 +2,14 @@
 import re
 from zipfile import ZipFile
 from functools import reduce
-from typing import Union, Sequence, Iterator, Optional
+from typing import Union, Sequence, Iterator
 
 from r_qtl import errors as rqe
 from r_qtl import r_qtl2 as rqtl2
 from r_qtl.r_qtl2 import __FILE_TYPES__
+from r_qtl.fileerrors import MissingFile
+
+from quality_control.errors import InvalidValue
 
 def bundle_files_list(cdata: dict) -> tuple[str, ...]:
     """Retrieve files listed in control file."""
@@ -56,8 +59,7 @@ def validate_bundle(zfile: ZipFile):
                         "The following files do not exist in the bundle: " +
                         ", ".join(missing))
 
-def geno_errors(zfile: ZipFile) -> Iterator[
-        tuple[Optional[int], Optional[str], str]]:
+def geno_errors(zfile: ZipFile) -> Iterator[Union[InvalidValue, MissingFile]]:
     """Check for and retrieve geno errors."""
     cdata = rqtl2.control_data(zfile)
     genotypes = tuple(cdata.get("genotypes", {}).keys())
@@ -68,13 +70,14 @@ def geno_errors(zfile: ZipFile) -> Iterator[
                 if field == "id":
                     continue
                 if value is not None and value not in genotypes:
-                    yield (lineno, field, (
-                        f"Invalid value '{value}'. Expected one of {genotypes}"))
+                    yield InvalidValue(lineno, field, value, (
+                        f"Invalid value '{value}'. Expected one of "
+                        f"{genotypes}."))
     except rqe.MissingFileError:
-        yield (None, None, "Missing 'geno' file.")
+        fname = cdata.get("geno")
+        yield MissingFile("geno", fname, f"Missing 'geno' file '{fname}'.")
 
-def pheno_errors(zfile: ZipFile) -> Iterator[
-        tuple[Optional[int], Optional[str], str]]:
+def pheno_errors(zfile: ZipFile) -> Iterator[Union[InvalidValue, MissingFile]]:
     """Check for and retrieve pheno errors."""
     cdata = rqtl2.control_data(zfile)
     try:
@@ -87,8 +90,9 @@ def pheno_errors(zfile: ZipFile) -> Iterator[
                         re.search(r"^([0-9]+\.[0-9]{3,}|[0-9]+\.?0*)$", value)
                         or re.search(r"^0\.0+$", value)
                         or re.search("^0+$", value)):
-                    yield (lineno, field, (
+                    yield InvalidValue(lineno, field, value, (
                         f"Invalid value '{value}'. Expected numerical value "
                         "with at least 3 decimal places."))
     except rqe.MissingFileError:
-        yield (None, None, "Missing 'pheno' file.")
+        fname = cdata.get("pheno")
+        yield MissingFile("pheno", fname, f"Missing 'pheno' file '{fname}'.")
diff --git a/tests/r_qtl/test_r_qtl2_qc.py b/tests/r_qtl/test_r_qtl2_qc.py
index 1c96a86..554cfc4 100644
--- a/tests/r_qtl/test_r_qtl2_qc.py
+++ b/tests/r_qtl/test_r_qtl2_qc.py
@@ -6,6 +6,9 @@ from zipfile import ZipFile
 
 from r_qtl import r_qtl2 as rqtl2
 from r_qtl import r_qtl2_qc as rqc
+from r_qtl.fileerrors import MissingFile
+
+from quality_control.errors import InvalidValue
 
 @pytest.mark.unit_test
 @pytest.mark.parametrize(
@@ -85,13 +88,13 @@ def test_missing_files(filepath, expected):
 @pytest.mark.parametrize(
     "filepath,expected",
     (("tests/r_qtl/test_files/empty_control_file_yaml.zip",
-      ((None, None, "Missing 'geno' file."),)),
+      (MissingFile("geno", None, "Missing 'geno' file 'None'."),)),
      ("tests/r_qtl/test_files/test_geno.zip",
       tuple()),
      ("tests/r_qtl/test_files/geno_with_missing_genotypes.zip",
-      ((1, "AXR-1", "Invalid value 'X'. Expected one of ('L', 'C')"),
-       (2, "EC.480C", "Invalid value 'Y'. Expected one of ('L', 'C')"),
-       (6, "HH.335C-Col/PhyA", f"Invalid value 'H'. Expected one of ('L', 'C')")))))
+      (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').")))))
 def test_geno_errors(filepath, expected):
     """
     GIVEN: A R/qtl2 bundle
@@ -106,14 +109,14 @@ def test_geno_errors(filepath, expected):
 @pytest.mark.parametrize(
     "filepath,expected",
     (("tests/r_qtl/test_files/empty_control_file_yaml.zip",
-      ((None, None, "Missing 'pheno' file."),)),
+      (MissingFile("pheno", None, "Missing 'pheno' file 'None'."),)),
      ("tests/r_qtl/test_files/pheno_without_errors.zip",
       tuple()),
      ("tests/r_qtl/test_files/pheno_with_errors.zip",
-      ((1, "liver", ("Invalid value '61.92'. Expected numerical value "
-                     "with at least 3 decimal places.")),
-       (2, "spleen", ("Invalid value 'brrr'. Expected numerical value "
-                     "with at least 3 decimal places."))))))
+      (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."))))))
 def test_pheno_errors(filepath, expected):
     """
     GIVEN: A R/qtl2 bundle
-- 
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