Add Serialisation Support #31
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ctb
reviewed
Sep 18, 2024
Cargo.toml
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| @@ -14,3 +14,10 @@ sourmash = "0.15.1" | |||
| anyhow = "1.0.89" | |||
| log = "0.4.22" | |||
| env_logger = "0.11.5" | |||
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| # For JSON serialization/deserialization | |||
| serde = { version = "1.0", features = ["derive"] } | |||
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why version 1? latest is 1.0.210. (presumably dependabot will upgrade, just curious.)
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No good reason, just inherited from example code.
ctb
reviewed
Sep 18, 2024
Cargo.toml
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| serde_json = "1.0" | ||
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| # For Gzip compression/decompression | ||
| flate2 = "1.0" |
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suggest niffler, which allows sniffing/auto-determination of file formats. but we can backport that in if we need.
(I'm using it over in #10)
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Will look into niffler 👍
Only ever expecting gzipped JSON as input.
ctb
approved these changes
Sep 18, 2024
|
Hey @ctb, can you look over the niffler changes. It passes all my tests, but the code is a bit rough, especially with the error handling. Any additional test case suggestion welcome. |
* Do format updates on top of current commit rather than head. (#46) * update serde_json version * switch to using built-in temp_path * write two additional tests * Style fixes by Ruff * clean up docstrings viz cargo doc --document-private-items --------- Co-authored-by: Adam Taranto <[email protected]> Co-authored-by: ctb <[email protected]>
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Add serialisation support for
KmerCountTableobjects using Serde.New methods:
.serialize_json()this will serialise a count table to JSON format, returns raw JSON string. Mostly useful for testing..save("counts.json.gz")this will convert a count table to JSON format, compress it with gzip, and write to a target file..load()is a static method that will load a count table saved injson.gzformat and return a newKmerCountTablewith the loaded properties. Raises a warning if Oxli version of the saved object is different to the current version.Closes #25