Rust DAT parser #39
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Rust DAT parser #39
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rien
reviewed
Jan 31, 2024
scripts/helper_scripts/unipept-database-rs/src/dat_parser/threaded_parser.rs
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scripts/helper_scripts/unipept-database-rs/src/dat_parser/threaded_parser.rs
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scripts/helper_scripts/unipept-database-rs/src/dat_parser/sequential_parser.rs
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scripts/helper_scripts/unipept-database-rs/src/dat_parser/entry.rs
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…ential_parser.rs Co-authored-by: Rien <[email protected]>
rien
approved these changes
Feb 5, 2024
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I created my own parser for Uniprot's custom DAT file format. This format is completely undocumented, so I had to reverse-engineer it by comparing it to an XML file. I have made notes of my findings and added them in a markdown file for you to reference in the future.
My parser is very heavily based on the
uniprot-rslibrary we're using for the XML parser, as writing threaded parsers is quite difficult and I had never done it before.The parser includes both a simple single-threaded parser, as well as a (far) more complex multi-threaded parser. The multi-threaded parser is only a few hundredths of a second faster than the single-threaded one, so I have left the simple single-threaded parser in as well because it's easier to work with and expand upon.
As a bonus, I introduced unit tests into the project :) There were none before, and I felt like the parser warranted it because it heavily exploits the structure of the DAT file. Testing was added to the CI as well.