feat: BMG Mars - Updated parser to support BMG Labtech format (#1126)

Co-authored-by: joshua-benchling <jherna@benchling.com>

Author: felipenarv

src/allotropy/parsers/bmg_mars/bmg_mars_reader.py

@@ -28,6 +28,12 @@ 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"))
+        # Some headers may include an extra trailing comma at the end of a line.
+        # Remove a single trailing comma from any header line before reading.
+        lines = [
+            (line[:-1].rstrip() if line.rstrip().endswith(",") else line)
+            for line in lines
+        ]
         # Store the header contents so we can parse some values that don't have key/value
         # pairs such as wavelengths and read type.
         self.header_content = "\n".join(lines)

src/allotropy/parsers/bmg_mars/bmg_mars_structure.py

@@ -74,6 +74,10 @@ class Header:
             r"Raw Data \((\d+\.?\d*)/(\d+\.?\d*)\)",
             lambda m: (float(m.group(2)), float(m.group(1))),
         ),
+        "Raw Data (Ex Em)": (
+            r"Raw Data \((\d+\.?\d*) (\d+\.?\d*)\)",
+            lambda m: (float(m.group(2)), float(m.group(1))),
+        ),
         "Raw Data (Em)": (
             r"Raw Data \((\d+\.?\d*)\)",
             lambda m: (float(m.group(1)), None),

tests/parsers/bmg_mars/testdata/BMG Labtech format.CSV

@@ -0,0 +1,17 @@
+User: Discovery,Path: C:\Users\Lab user\Documents\Discovery\Data,Test run no.: 445
+Test name: xxxxxxxxxxxxx,Date: 5/14/2021,Time: 3:29:50 PM
+
+ID1: xxxxxxxxxxxxx,ID2: Plate 1,ID3: xxxxxxx 11/5/21,
+Absorbance
+
+Raw Data (450 1)
+
+,1,2,3,4,5,6,7,8,9,10,11,12,
+A,0.073,0.082,0.08,0.107,0.103,0.111,0.199,0.159,0.104,0.096,0.092,0.089
+B,0.045,0.067,0.012,0.118,0.1,0.086,0.188,0.112,0.124,0.181,0.218,0.23
+C,0.502,0.065,0.012,0.656,0.501,0.132,0.111,0.142,0.71,0.581,0.541,0.596
+D,0.121,0.121,0.37,0.634,0.677,0.606,0.069,0.666,0.054,0.836,0.149,0.168
+E,0.109,0.06,0.09,0.07,0.072,0.059,0.079,0.073,0.062,0.121,0.112,0.112
+F,0.072,0.012,0.064,0.012,0.061,0.06,0.079,0.088,0.082,0.012,0.068,0.1
+G,0.314,0.056,0.057,0.376,0.411,0.075,0.081,0.091,0.121,0.41,0.212,0.212
+H,0.422,0.224,0.115,0.278,0.377,0.385,0.056,0.377,0.107,0.462,0.116,0.207