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Fix column order validation #182

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merged 4 commits into from
Oct 11, 2024
Merged

Fix column order validation #182

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be657f5
Fix column order validation
Oct 9, 2024
f6f3617
Black reformat
Oct 9, 2024
ee678ad
Implement new rules for technology type
Oct 11, 2024
0e132fc
black reformat
Oct 11, 2024
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34 changes: 23 additions & 11 deletions sdrf_pipelines/sdrf/sdrf_schema.py
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Original file line number Diff line number Diff line change
Expand Up @@ -280,19 +280,31 @@ def validate_columns_order(panda_sdrf):
error_columns_order = []
if "assay name" in list(panda_sdrf):
cnames = list(panda_sdrf)
index = cnames.index("assay name")
assay_index = cnames.index("assay name")
factor_tag = False
for column in cnames:
if ("comment" in column or "technology type" in column) and cnames.index(column) < index:
error_message = "The column " + column + "cannot be before the assay name"
error_columns_order.append(LogicError(error_message, error_type=logging.ERROR))
if (
"characteristics" in column or ("material type" in column and "factor value" not in column)
) and cnames.index(column) > index:
error_message = "The column " + column + "cannot be after the assay name"
error_columns_order.append(LogicError(error_message, error_type=logging.ERROR))
for idx, column in enumerate(cnames):
error_message, error_type = "", None
if idx < assay_index:
if "comment" in column:
error_message = "The column " + column + " cannot be before the assay name"
error_type = logging.ERROR
if "technology type" in column:
error_message = "The column " + column + " must be immediately after the assay name"
if assay_index - idx > 1:
error_type = logging.ERROR
else:
error_type = logging.WARNING
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else:
if "characteristics" in column or ("material type" in column and "factor value" not in column):
error_message = "The column " + column + " cannot be after the assay name"
error_type = logging.ERROR
if "technology type" in column and idx > assay_index + 1:
error_message = "The column " + column + " must be immediately after the assay name"
error_type = logging.ERROR
if error_type is not None:
error_columns_order.append(LogicError(error_message, error_type=error_type))
if "factor value" in column and not factor_tag:
factor_index = cnames.index(column)
factor_index = idx
factor_tag = True
if factor_tag:
temp = []
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