Various bug fixes.
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@@ -35,7 +35,7 @@ class SheetParser(object):
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Args:
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filepath (Path | None, optional): file path to excel sheet. Defaults to None.
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"""
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logger.debug(f"\n\nParsing {filepath.__str__()}\n\n")
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logger.info(f"\n\nParsing {filepath.__str__()}\n\n")
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match filepath:
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case Path():
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self.filepath = filepath
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@@ -651,6 +651,15 @@ class PCRParser(object):
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info_map = self.submission_obj.get_submission_type().sample_map['pcr_general_info']
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sheet = self.xl[info_map['sheet']]
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iter_rows = sheet.iter_rows(min_row=info_map['start_row'], max_row=info_map['end_row'])
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pcr = {row[0].value.lower().replace(' ', '_'): row[1].value for row in iter_rows}
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pcr = {}
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for row in iter_rows:
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try:
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key = row[0].value.lower().replace(' ', '_')
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except AttributeError as e:
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logger.error(f"No key: {row[0].value} due to {e}")
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continue
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value = row[1].value or ""
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pcr[key] = value
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pcr['imported_by'] = getuser()
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# logger.debug(f"PCR: {pformat(pcr)}")
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return pcr
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