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fix: use external sort during clinvar-genes import #640

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merged 11 commits into from
Jan 30, 2025
Merged

fix: use external sort during clinvar-genes import #640

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b56d74a
use extsort during clinvar genes import
tedil Jan 28, 2025
b2e7073
use rmp::write_named_vec so decoding actually works without problems
tedil Jan 29, 2025
3ffe4d4
use into_group_map_by instead of chunk_by
tedil Jan 29, 2025
d522cab
fix wording
tedil Jan 29, 2025
120c1de
use multigzdecoder + bufread of flate2 crate
tedil Jan 29, 2025
f8ce36d
no need to sort at this point
tedil Jan 29, 2025
c34f3ac
manually distribute records to $HGNC_ID.jsonl.gz for sorting
tedil Jan 29, 2025
4caecbb
remove unused imports
tedil Jan 29, 2025
99a0dc9
remove detailed progress prints
tedil Jan 29, 2025
6e61733
use LRU cache for writers; use subdirectories to reduce #files/dir
tedil Jan 30, 2025
5b2df2c
add ANNONARS_CLINVAR_GENES_IMPORT_CACHE_SIZE env var for controlling …
tedil Jan 30, 2025
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34 changes: 31 additions & 3 deletions Cargo.lock
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4 changes: 2 additions & 2 deletions Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -55,6 +55,8 @@ tracing = "0.1"
tracing-subscriber = "0.3"
utoipa-swagger-ui = { version = "8.0", features = ["actix-web"] }
utoipa = { version = "5.2", features = ["actix_extras", "chrono", "indexmap", "preserve_order", "yaml"] }
tempfile = "3.10.1"
lru = "0.13.0"

[dependencies.noodles]
version = "0.77.0"
Expand All @@ -78,5 +80,3 @@ tracing-test = "0.2.4"
# Compile insta with full optimization.
[profile.dev.package.insta]
opt-level = 3
[profile.dev.package.similar]
opt-level = 3
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