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Opaque error when data sources is missing a column #46

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jakebeal opened this issue Oct 14, 2021 · 3 comments · May be fixed by #236
Open

Opaque error when data sources is missing a column #46

jakebeal opened this issue Oct 14, 2021 · 3 comments · May be fixed by #236
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bug Something isn't working good first issue Good for newcomers

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@jakebeal
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When the "data sources" tab is missing a column (e.g., column G on old versions of the sheet), it exceptions with an opaque error:

>>> doc = es.excel_to_sbol(wb)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Python39\site-packages\sbol_utilities\excel_to_sbol.py", line 426, in excel_to_sbol
    basic_parts, composite_parts, linear_products, final_products, source_table = read_metadata(wb, doc, config)
  File "C:\Python39\site-packages\sbol_utilities\excel_to_sbol.py", line 110, in read_metadata
    source_table = {row[config['source_name_col']].value: row[config['source_uri_col']].value
  File "C:\Python39\site-packages\sbol_utilities\excel_to_sbol.py", line 112, in <dictcomp>
    if row[config['source_literal_col']].value}
IndexError: tuple index out of range

It should at least be more graceful about its crash.
@jakebeal jakebeal added the bug Something isn't working label Oct 14, 2021
@jakebeal
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There is a similar issue when there are extra columns not expected, thus causing a problem in interpretation.

@jakebeal jakebeal added this to the 1.0a13 milestone Oct 28, 2021
@jakebeal jakebeal added the good first issue Good for newcomers label Jan 17, 2022
@jakebeal jakebeal removed this from the 1.0a14 milestone Jan 18, 2022
@mohitdmak
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Hello @jakebeal , enclosing the part of reading_metadata where it fetches the G column (Literal part) in a try block seems to handle this, shouldn't this be all that's needed? Also, can you describe the issue of parsing with extra columns? I am not able to reproduce it by editing the simple library xl file.

@jakebeal
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@mohitdmak I'm not surprised if it's a fairly simple fix.

For the extra columns, example, try inserting some columns in the middle with new names. I don't think it's being smart enough to handle it. If it is, though, then add a test case to validate and we're good.

@vinayakjeet vinayakjeet linked a pull request Apr 1, 2024 that will close this issue
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Enhanced Error Handling for Missing Columns in Excel Input vinayakjeet/SBOL-utilities
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@jakebeal @mohitdmak