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fix: MSD Methodical Mind - support wells larger than 192 wells correctly #1009

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Merged
nathan-stender merged 3 commits into from
Jun 10, 2025
Merged

fix: MSD Methodical Mind - support wells larger than 192 wells correctly #1009

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95140ee
Add support for 384 wells
nathan-stender Jun 10, 2025
c19deaf
Add new test file
nathan-stender Jun 10, 2025
141260f
Fix typing
nathan-stender Jun 10, 2025
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11 changes: 7 additions & 4 deletions src/allotropy/parsers/methodical_mind/methodical_mind_structure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
from collections import defaultdict
from dataclasses import dataclass
from pathlib import Path
import re
from typing import Any

import pandas as pd
Expand All @@ -18,8 +19,6 @@
from allotropy.parsers.utils.pandas import SeriesData
from allotropy.parsers.utils.uuids import random_uuid_str

WELL_LABELS = ["A", "B", "C", "D", "E", "F", "G", "H"]


@dataclass(frozen=True)
class Header:
Expand All @@ -38,6 +37,10 @@ def create(data: SeriesData) -> Header:
)


def _is_valid_well_label(label: str) -> bool:
return bool(re.match("[A-Z]+", label))


@dataclass(frozen=True)
class PlateData:
measurement_time: str
Expand All @@ -56,7 +59,7 @@ def create(
) -> PlateData:
well_plate_id = header[str, "Barcode1"].strip("<>")
unique_well_labels = [
label for label in data.index.unique() if label in WELL_LABELS
label for label in data.index.unique() if _is_valid_well_label(label)
]
spot_id = header.get(int, "SpotID")
well_data = [
Expand All @@ -70,7 +73,7 @@ def create(
for row_name in unique_well_labels
for row_index, (_, row) in enumerate(data.loc[[row_name]].iterrows())
for col_name, value in row.items()
if row_name in WELL_LABELS
if _is_valid_well_label(row_name)
# Only include if the measurement is not an empty string, this skips blank entries for non-visible
# measurements.
if str(value).strip()
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