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fix: ChemoMetec Nucleoview - wrap key error when indexing dataframe #1006

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Merged
nathan-stender merged 2 commits into from
Jun 10, 2025
Merged

fix: ChemoMetec Nucleoview - wrap key error when indexing dataframe #1006

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5474cd3
wrap key error when indexing dataframe
joshua-benchling Jun 4, 2025
8634471
Merge branch 'main' into jherna-chemometec-nucleo-view
nathan-stender Jun 10, 2025
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9 changes: 7 additions & 2 deletions src/allotropy/parsers/chemometec_nucleoview/nucleoview_reader.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
import pandas as pd

from allotropy.exceptions import AllotropeConversionError
from allotropy.exceptions import AllotropeConversionError, AllotropeParsingError
from allotropy.parsers.utils.pandas import assert_not_empty_df, read_csv
from allotropy.types import IOType

Expand All @@ -13,7 +13,12 @@ def read(cls, contents: IOType) -> pd.DataFrame:
df = read_csv(
contents, sep="[;,]+", engine="python", skipinitialspace=True, index_col=0
)
df = df[:-1].dropna(axis="index", how="all").T
try:
df = df[:-1].dropna(axis="index", how="all").T
except KeyError as e:
msg = f"Error processing CSV data structure. The file may be corrupted or have an invalid format: {e}"
raise AllotropeParsingError(msg) from e

df = df.rename(
{"Estimated cell diameter [um]": "Estimated cell diameter (um)"},
axis="columns",
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