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/r_qtl2_qc.py | 24 ++++++++++++++----------
 1 file changed, 14 insertions(+), 10 deletions(-)

(limited to 'r_qtl/r_qtl2_qc.py')

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}'.")
-- 
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