fix: BMG Mars: wrap keyError when index out of range (#1005)

Co-authored-by: Nathan Stender <nathan.stender@benchling.com>

Author: joshua-benchling

src/allotropy/parsers/bmg_mars/bmg_mars_reader.py

@@ -2,6 +2,7 @@
 
 import pandas as pd
 
+from allotropy.exceptions import AllotropeConversionError
 from allotropy.named_file_contents import NamedFileContents
 from allotropy.parsers.lines_reader import CsvReader, read_to_lines
 from allotropy.parsers.utils.pandas import read_csv, SeriesData
@@ -27,6 +28,11 @@ def __init__(self, named_file_contents: NamedFileContents) -> None:
             axis="index"
         )
         new = df["value"].str.split(": ", expand=True, n=1)
+
+        # Handle the case where no ": " delimiter is found, resulting in a DataFrame with only one column
+        if new.shape[1] < 2:
+            msg = "Unable to parse header data: no key-value pairs found with expected format."
+            raise AllotropeConversionError(msg)
         self.header = SeriesData(pd.Series(new[1].values, index=new[0].str.upper()))
 
         # Read in the rest of the file as a dataframe

tests/parsers/bmg_mars/testdata/errors/file_with_no_delimiter_malformed.csv

@@ -0,0 +1,25 @@
+User = USER,Path = C:\Program Files (x86)\BMG\PHERAstar\User\Data,Test run no. = 1,,,,,,,,,,,,,,,,,,,,,,
+Test name = 472 QC 384 FI,Date = 03/03/2016,Time = 13:25:45,,,,,,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,,,,,,,
+ID1 = 472-0016,,,,,,,,,,,,,,,,,,,,,,,,
+Fluorescence (FI),,,,,,,,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,,,,,,,
+Raw Data (485/520),,,,,,,,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,,,,,,,
+,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24
+A,23864,23796,23934,,,,,,,,,231438,228111,,,,,,,,,24069,24096,24098
+B,23774,23887,23810,,,,,,,,,229790,230207,,,,,,,,,24121,24223,24106
+C,23879,23687,23567,,,,,,,,,2682,2677,,,,,,,,,24171,24104,23987
+D,,,,,,,,,,,,2679,2661,,,,,,,,,,,
+E,,,,,,,,,,,,371,374,,,,,,,,,,,
+F,,,,,,,,,,,,372,375,,,,,,,,,,,
+G,,,,,,,,,,,,187,183,,,,,,,,,,,
+H,,,,,,,,,,,,187,188,,,,,,,,,,,
+I,,,,,,,,,,,,123,118,,,,,,,,,,,
+J,,,,,,,,,,,,120,120,,,,,,,,,,,
+K,,,,,,,,,,,,120,124,,,,,,,,,,,
+L,,,,,,,,,,,,122,121,,,,,,,,,,,
+M,,,,,,,,,,,,119,121,,,,,,,,,,,
+N,23478,23579,23326,,,,,,,,,118,120,,,,,,,,,23650,23767,23705
+O,23730,23719,23988,,,,,,,,,122,121,,,,,,,,,23904,23959,24076
+P,23488,23724,23895,,,,,,,,,120,120,,,,,,,,,23715,23502,23949

tests/parsers/bmg_mars/to_allotrope_test.py

@@ -1,6 +1,25 @@
+import pytest
+
+from allotropy.constants import CHARDET_ENCODING
+from allotropy.exceptions import AllotropeConversionError
 from allotropy.parser_factory import Vendor
+from allotropy.testing.utils import from_file, get_testdata_dir
 from tests.to_allotrope_test import ParserTest
 
+TESTDATA = get_testdata_dir(__file__)
+
 
 class TestParser(ParserTest):
     VENDOR = Vendor.BMG_MARS
+
+
+def test_to_allotrope_unsupported_kinetic_file() -> None:
+    with pytest.raises(
+        AllotropeConversionError,
+        match="Unable to parse header data: no key-value pairs found with expected format.",
+    ):
+        from_file(
+            f"{TESTDATA}/errors/file_with_no_delimiter_malformed.csv",
+            TestParser.VENDOR,
+            encoding=CHARDET_ENCODING,
+        )