Added dynamic section restructuring for non-PMC articles. #20
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…quality improvements, as well as a major refactoring of the Tables.py code design. Python code throughout AC has been mostly standardised with PEP compliance, however more work will be needed to cover the entire code base. Bugs Fixed: - Offset incorrect for the first "data_section" - HTML comments present in AC output. - Table title offset should now correct. - Offset value is now assigned to 'table_section_title'. - Empty 'table_section_title' fields are no longer output. - Removed duplicate pipe characters from table headers. - Table header strings should now display in the correct order, separated by pipes. - The first column has returned to the table outputs, even with no cell values. - Corrected ordering of data section rows. - Table footers are now duplicated for each split table output. - Tables should now split into multiple smaller tables under the correct circumstances; when encountering subheaders. - Super rows will no longer cause tables to be split.
…ong with their accompanying links).
…some scenarios (e.g. PMC4294952).
…ping on the first failed PMC file.
# Conflicts: # configs/config_pmc.json # run_app.py # src/AutoCorpus.py # src/table.py # src/utils.py
…putting texts regardless of table extraction results.
…putting texts regardless of table extraction results.
# Conflicts: # run_app.py # src/AutoCorpus.py # src/excel_extractor.py # src/pdf_extractor.py # src/supplementary_processor.py
# Conflicts: # src/bioc_documents.py
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Re-using this PR since it is based on the same branch of my fork. This now includes a merge of all existing branches within my fork (see changes above). Main changes |
# Conflicts: # src/bioc_documents.py
Updated the github action to ensure poetry is installed initially
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Sections from journals such as Human Molecular Genetics were not cleanly contained separately, instead just having their contents listed all as siblings throughout the main text.
This update restructures matches that display this type of layout, then restructures them into empty parent divs more akin to PMC articles. The rest of the AC code base can then treat matches in the same manner as before effectively.
White space removal has been commented out for now until a few kinks are worked out.