feat: BMG Mars - Support for CSVs generated by Mars V3.40 R2 (#1105)

BMG Mars V3.40 R2 generates malformed CSVs that have missing end of line
separators. This PR adds support to enable successful parsing of those
files.

A test case was added, adapted from another test case, more real tests
be provided if required

Author: Cynicjon

src/allotropy/parsers/bmg_mars/bmg_mars_reader.py

@@ -1,3 +1,4 @@
+import csv
 from io import StringIO
 
 import pandas as pd
@@ -16,6 +17,15 @@ class BmgMarsReader:
     header_content: str
 
     def __init__(self, named_file_contents: NamedFileContents) -> None:
+        try:
+            self._parse_file(named_file_contents)
+        except pd.errors.ParserError:
+            # Fix malformed CSV files with uneven columns and retry
+            named_file_contents = self._normalize_csv_columns(named_file_contents)
+            self._parse_file(named_file_contents)
+
+    def _parse_file(self, named_file_contents: NamedFileContents) -> None:
+        """Parse the BMG MARS file and populate header and data attributes."""
         reader = CsvReader(read_to_lines(named_file_contents))
         lines = list(reader.pop_until_inclusive("^,?Raw Data"))
         # Store the header contents so we can parse some values that don't have key/value
@@ -28,7 +38,6 @@ 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."
@@ -41,3 +50,67 @@ def __init__(self, named_file_contents: NamedFileContents) -> None:
             reader.pop_csv_block_as_df(header=0, index_col=0),
             msg="Unable to parse dataset from file.",
         )
+
+    def _normalize_csv_columns(
+        self, named_file_contents: NamedFileContents
+    ) -> NamedFileContents:
+        """Fix malformed CSV files with uneven number of columns per row.
+
+        BMG MARS software <= v4.0 can produce CSV files where some rows have
+        more or fewer columns than others. This method normalizes all rows
+        to have the same number of columns by padding with empty strings,
+        allowing the csv reader to parse the file correctly.
+
+        Args:
+            named_file_contents: The named file contents to fix
+
+        Returns:
+            Fixed NamedFileContents with consistent column counts
+        """
+        lines = read_to_lines(named_file_contents)
+
+        if not lines:
+            return named_file_contents
+
+        # Parse all rows and find the maximum number of columns
+        csv_rows = []
+        max_columns = 0
+
+        for line in lines:
+            if line.strip():
+                reader = csv.reader([line])
+                try:
+                    row = next(reader)
+                    csv_rows.append(row)
+                    max_columns = max(max_columns, len(row))
+                except (csv.Error, StopIteration):
+                    # If parsing fails, keep the original line
+                    csv_rows.append([line])
+                    max_columns = max(max_columns, 1)
+            else:
+                pass  # skip empty lines
+
+        # Normalize all rows to have the same number of columns
+        normalized_rows = []
+        for row in csv_rows:
+            normalized_row = row.copy()
+            if len(normalized_row) < max_columns:
+                # Pad with empty strings
+                normalized_row.extend([""] * (max_columns - len(normalized_row)))
+            elif len(normalized_row) > max_columns:
+                # Truncate if somehow longer (shouldn't happen with max calculation)
+                normalized_row = normalized_row[:max_columns]
+            normalized_rows.append(normalized_row)
+
+        # Convert back to CSV string
+        output = StringIO()
+        writer = csv.writer(output)
+        writer.writerows(normalized_rows)
+        output.seek(0)
+
+        # Create a new NamedFileContents with the fixed content
+        return NamedFileContents(
+            contents=output,
+            original_file_path=named_file_contents.original_file_path,
+            encoding="utf-8",
+        )

tests/parsers/bmg_mars/testdata/MARS V3.40 V2 Output Missing line end separators.csv

@@ -0,0 +1,25 @@
+User: USER,Path: C:\Program Files (x86)\BMG\PHERAstar\User\Data,Test run no.: 4
+Test name: Transcreener ADP2 FI,Date: 29/02/2016,Time: 14:34:46
+
+ID1: black 384w small volume,ID2: 20 ul
+Fluorescence (FI)
+
+Raw Data (580/620)
+
+,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,25104,25203,24886,24098,24466,26571,24056,24156,24130,24089,21634,21969,22160,23823,23019,22230,22992,23852,23657,24361
+B,33863,33227,34758,33603,34186,34318,34196,35279,35608,37342,35468,34056,34031,33235,33242,33304,35286,34482,34378,33774
+C,45480,42551,41891,44773,43821,45338,43328,42901,44137,46425,39341,39162,39791,41566,41265,43889,40461,41195,40761,40262
+D,50970,50862,50279,50797,51063,50202,50808,50966,50097,49497,50325,48821,48954,49208,49181,49016,49404,49271,48856,47830
+E,53997,52824,53844,50679,55121,54280,53994,54413,54396,53971,53444,50748,53143,53916,53624,53156,53531,53493,53216,53154
+F,55774,56191,56164,56462,55583,56253,56300,55464,56719,54927,56253,54441,58358,56279,55870,55886,55465,55897,55737,53798
+G,57378,57180,57681,58158,57949,57397,57546,57895,58077,57617,57827,57072,58385,58021,58624,57891,57835,58321,58046,55748
+H,59660,58847,59844,60655,61534,60652,60090,60958,59683,59631,59656,58141,59493,59990,59664,59956,59928,60272,59780,58810
+I,63183,57522,58573,60240,60618,60777,61149,61504,61682,60194,61840,61912,61256,63237,61643,60385,60806,60566,60231,58425
+J,62375,61292,62851,65025,64750,65573,58147,64039,63962,64279,64763,60451,64021,64272,65055,63228,61028,61503,61899,60751
+K,63255,63635,63048,63799,65845,66218,65161,63773,64427,62842,65316,64136,65885,65606,65812,66198,62934,63653,64950,62926
+L,66220,62882,65007,64797,65385,66359,66227,67120,65709,64827,65253,61630,66214,65540,65774,67329,65779,65519,65672,63404
+M,63792,64859,66378,66579,67777,67381,67099,67971,66080,64760,67145,65628,66682,66075,66363,65642,67384,65322,63597,64895
+N,64497,64888,64056,65284,66138,66751,66896,66044,66878,62160,64748,64183,65883,65153,66413,63789,63507,62883,63665,63882
+O,68426,60666,65656,66138,63289,107,103,98,100,94,,59
+P,63471,62852,62886,63555,63035,79,90,100,102,103,,62