Stream mode FileNotFound exception handling
Browse files- pmc_open_access_xml.py +4 -1
pmc_open_access_xml.py
CHANGED
@@ -533,7 +533,10 @@ class OpenAccessXML(datasets.GeneratorBasedBuilder):
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# Incrementals
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if incremental_file_lists:
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for incremental_file_list, incremental_archive in zip(incremental_file_lists[::-1], incremental_archives[::-1]):
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-
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incrementals = incrementals.join(oa_package_list).reset_index().set_index("Article File")
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incrementals.File = incrementals.File.fillna('')
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incrementals = incrementals.to_dict(orient="index")
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# Incrementals
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if incremental_file_lists:
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for incremental_file_list, incremental_archive in zip(incremental_file_lists[::-1], incremental_archives[::-1]):
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+
try:
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incrementals = pd.read_csv(incremental_file_list, index_col="AccessionID")
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except FileNotFoundError: # File not found can happen here in stream mode
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continue
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incrementals = incrementals.join(oa_package_list).reset_index().set_index("Article File")
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incrementals.File = incrementals.File.fillna('')
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incrementals = incrementals.to_dict(orient="index")
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