diff --git a/Cargo.lock b/Cargo.lock index 1efba14e..f6d9cec0 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -318,8 +318,55 @@ dependencies = [ "thiserror 1.0.69", "tracing", "tracing-subscriber", - "utoipa", - "utoipa-swagger-ui", + "utoipa 4.2.3", + "utoipa-swagger-ui 7.1.0", +] + +[[package]] +name = "annonars" +version = "0.42.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "86428b1ff21f6e8f5fc574928a3dc643300f4ddd4915eaed3f2c8cd47d0d5f79" +dependencies = [ + "actix-web", + "anyhow", + "bgzip", + "bio", + "biocommons-bioutils", + "boolvec", + "byteorder", + "chrono", + "clap", + "clap-verbosity-flag 2.2.3", + "csv", + "enum-map", + "env_logger", + "erased-serde", + "flate2", + "indexmap 2.7.0", + "indicatif", + "itertools 0.13.0", + "log", + "noodles 0.77.0", + "pbjson", + "pbjson-build", + "pbjson-types", + "prost", + "prost-build", + "rayon", + "rocksdb", + "rocksdb-utils-lookup", + "rustc-hash 2.0.0", + "serde", + "serde_json", + "serde_with", + "serde_yaml", + "strum", + "thiserror 2.0.3", + "tracing", + "tracing-subscriber", + "utoipa 5.2.0", + "utoipa-swagger-ui 8.0.3", ] [[package]] @@ -1211,6 +1258,18 @@ dependencies = [ "serde", ] +[[package]] +name = "built" +version = "0.7.5" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "c360505aed52b7ec96a3636c3f039d99103c37d1d9b4f7a8c743d3ea9ffcd03b" +dependencies = [ + "cargo-lock", + "chrono", + "git2", + "semver 1.0.23", +] + [[package]] name = "bumpalo" version = "3.16.0" @@ -1332,9 +1391,9 @@ dependencies = [ [[package]] name = "cached" -version = "0.53.1" +version = "0.54.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b4d73155ae6b28cf5de4cfc29aeb02b8a1c6dab883cb015d15cd514e42766846" +checksum = "9718806c4a2fe9e8a56fd736f97b340dd10ed1be8ed733ed50449f351dc33cae" dependencies = [ "ahash 0.8.11", "cached_proc_macro", @@ -1363,6 +1422,19 @@ version = "0.1.1" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "ade8366b8bd5ba243f0a58f036cc0ca8a2f069cff1a2351ef1cac6b083e16fc0" +[[package]] +name = "cargo-lock" +version = "10.0.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "6469776d007022d505bbcc2be726f5f096174ae76d710ebc609eb3029a45b551" +dependencies = [ + "petgraph", + "semver 1.0.23", + "serde", + "toml", + "url", +] + [[package]] name = "cc" version = "1.1.15" @@ -2343,6 +2415,19 @@ version = "0.29.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "40ecd4077b5ae9fd2e9e169b102c6c330d0605168eb0e8bf79952b256dbefffd" +[[package]] +name = "git2" +version = "0.19.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "b903b73e45dc0c6c596f2d37eccece7c1c8bb6e4407b001096387c63d0d93724" +dependencies = [ + "bitflags", + "libc", + "libgit2-sys", + "log", + "url", +] + [[package]] name = "glob" version = "0.3.1" @@ -2451,9 +2536,9 @@ checksum = "7f24254aa9a54b5c858eaee2f5bccdb46aaf0e486a595ed5fd8f86ba55232a70" [[package]] name = "hgvs" -version = "0.17.3" +version = "0.17.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e25a808a912191336fdfde6230ddaf4d154aaf49cbcc35d673544ba0fb2a3c93" +checksum = "049d7b9c42a2b7a2e814669e58e1c34a6825f64a7f2bc8863976ae60704d27ed" dependencies = [ "ahash 0.8.11", "base16ct 0.2.0", @@ -2475,7 +2560,7 @@ dependencies = [ "seqrepo", "serde", "serde_json", - "thiserror 1.0.69", + "thiserror 2.0.3", ] [[package]] @@ -2959,6 +3044,18 @@ version = "0.2.167" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "09d6582e104315a817dff97f75133544b2e094ee22447d2acf4a74e189ba06fc" +[[package]] +name = "libgit2-sys" +version = "0.17.0+1.8.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "10472326a8a6477c3c20a64547b0059e4b0d086869eee31e6d7da728a8eb7224" +dependencies = [ + "cc", + "libc", + "libz-sys", + "pkg-config", +] + [[package]] name = "libloading" version = "0.8.5" @@ -3018,6 +3115,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "d2d16453e800a8cf6dd2fc3eb4bc99b786a9b90c663b8559a5b1a041bf89e472" dependencies = [ "cc", + "libc", "pkg-config", "vcpkg", ] @@ -3061,6 +3159,12 @@ dependencies = [ "scopeguard", ] +[[package]] +name = "lockfree-object-pool" +version = "0.1.6" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "9374ef4228402d4b7e403e5838cb880d9ee663314b0a900d5a6aabf0c213552e" + [[package]] name = "log" version = "0.4.22" @@ -3131,17 +3235,18 @@ dependencies = [ [[package]] name = "mehari" -version = "0.29.6" +version = "0.30.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "813beab32532331615621ef04136e2e0f330bfb052ade27439ff96f479ba9634" +checksum = "b68862bce5d5c41002ea0db758938bb0d3ad5595e8835c38e50c689cde67d1ea" dependencies = [ "actix-web", - "annonars", + "annonars 0.41.3", "anyhow", "async-compression", "bgzip", "bio", "biocommons-bioutils", + "built", "byte-unit", "byteorder", "chrono", @@ -3172,7 +3277,7 @@ dependencies = [ "pbjson-build", "pbjson-types", "percent-encoding", - "procfs 0.16.0", + "procfs", "prost", "prost-build", "quick_cache", @@ -3192,6 +3297,9 @@ dependencies = [ "tokio", "tracing", "tracing-subscriber", + "utoipa 4.2.3", + "utoipa-actix-web", + "utoipa-swagger-ui 7.1.0", "uuid", "zstd", ] @@ -4081,21 +4189,6 @@ dependencies = [ "unicode-ident", ] -[[package]] -name = "procfs" -version = "0.16.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "731e0d9356b0c25f16f33b5be79b1c57b562f141ebfcdb0ad8ac2c13a24293b4" -dependencies = [ - "bitflags", - "chrono", - "flate2", - "hex", - "lazy_static", - "procfs-core 0.16.0", - "rustix", -] - [[package]] name = "procfs" version = "0.17.0" @@ -4106,21 +4199,10 @@ dependencies = [ "chrono", "flate2", "hex", - "procfs-core 0.17.0", + "procfs-core", "rustix", ] -[[package]] -name = "procfs-core" -version = "0.16.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2d3554923a69f4ce04c4a754260c338f505ce22642d3830e049a399fc2059a29" -dependencies = [ - "bitflags", - "chrono", - "hex", -] - [[package]] name = "procfs-core" version = "0.17.0" @@ -4908,6 +4990,9 @@ name = "semver" version = "1.0.23" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "61697e0a1c7e512e84a621326239844a24d8207b4669b41bc18b32ea5cbf988b" +dependencies = [ + "serde", +] [[package]] name = "seqrepo" @@ -4955,6 +5040,15 @@ dependencies = [ "serde", ] +[[package]] +name = "serde_spanned" +version = "0.6.8" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "87607cb1398ed59d48732e575a4c28a7a8ebf2454b964fe3f224f2afc07909e1" +dependencies = [ + "serde", +] + [[package]] name = "serde_test" version = "1.0.177" @@ -5097,6 +5191,12 @@ dependencies = [ "wide", ] +[[package]] +name = "simd-adler32" +version = "0.3.7" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "d66dc143e6b11c1eddc06d5c423cfc97062865baf299914ab64caa38182078fe" + [[package]] name = "simdutf8" version = "0.1.4" @@ -5501,11 +5601,26 @@ dependencies = [ "tokio", ] +[[package]] +name = "toml" +version = "0.8.19" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "a1ed1f98e3fdc28d6d910e6737ae6ab1a93bf1985935a1193e68f93eeb68d24e" +dependencies = [ + "serde", + "serde_spanned", + "toml_datetime", + "toml_edit", +] + [[package]] name = "toml_datetime" version = "0.6.8" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "0dd7358ecb8fc2f8d014bf86f6f638ce72ba252a2c3a2572f2a795f1d23efb41" +dependencies = [ + "serde", +] [[package]] name = "toml_edit" @@ -5514,6 +5629,8 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "583c44c02ad26b0c3f3066fe629275e50627026c51ac2e595cca4c230ce1ce1d" dependencies = [ "indexmap 2.7.0", + "serde", + "serde_spanned", "toml_datetime", "winnow", ] @@ -5751,7 +5868,31 @@ dependencies = [ "serde", "serde_json", "serde_yaml", - "utoipa-gen", + "utoipa-gen 4.3.0", +] + +[[package]] +name = "utoipa" +version = "5.2.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "514a48569e4e21c86d0b84b5612b5e73c0b2cf09db63260134ba426d4e8ea714" +dependencies = [ + "indexmap 2.7.0", + "serde", + "serde_json", + "serde_yaml", + "utoipa-gen 5.2.0", +] + +[[package]] +name = "utoipa-actix-web" +version = "0.1.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "b7eda9c23c05af0fb812f6a177514047331dac4851a2c8e9c4b895d6d826967f" +dependencies = [ + "actix-service", + "actix-web", + "utoipa 5.2.0", ] [[package]] @@ -5767,6 +5908,18 @@ dependencies = [ "syn 2.0.87", ] +[[package]] +name = "utoipa-gen" +version = "5.2.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "5629efe65599d0ccd5d493688cbf6e03aa7c1da07fe59ff97cf5977ed0637f66" +dependencies = [ + "proc-macro2", + "quote", + "regex", + "syn 2.0.87", +] + [[package]] name = "utoipa-swagger-ui" version = "7.1.0" @@ -5781,8 +5934,25 @@ dependencies = [ "serde", "serde_json", "url", - "utoipa", - "zip", + "utoipa 4.2.3", + "zip 1.1.4", +] + +[[package]] +name = "utoipa-swagger-ui" +version = "8.0.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "a5c80b4dd79ea382e8374d67dcce22b5c6663fa13a82ad3886441d1bbede5e35" +dependencies = [ + "actix-web", + "mime_guess", + "regex", + "rust-embed", + "serde", + "serde_json", + "url", + "utoipa 5.2.0", + "zip 2.2.1", ] [[package]] @@ -5812,7 +5982,7 @@ checksum = "5a84c137d37ab0142f0f2ddfe332651fdbf252e7b7dbb4e67b6c1f1b2e925101" name = "varfish-server-worker" version = "0.17.0" dependencies = [ - "annonars", + "annonars 0.42.3", "anyhow", "async-compression", "async-std", @@ -5851,7 +6021,7 @@ dependencies = [ "pbjson-build", "pbjson-types", "pretty_assertions", - "procfs 0.17.0", + "procfs", "prost", "prost-build", "rand", @@ -6354,6 +6524,37 @@ dependencies = [ "thiserror 1.0.69", ] +[[package]] +name = "zip" +version = "2.2.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "99d52293fc86ea7cf13971b3bb81eb21683636e7ae24c729cdaf1b7c4157a352" +dependencies = [ + "arbitrary", + "crc32fast", + "crossbeam-utils", + "displaydoc", + "flate2", + "indexmap 2.7.0", + "memchr", + "thiserror 2.0.3", + "zopfli", +] + +[[package]] +name = "zopfli" +version = "0.8.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "e5019f391bac5cf252e93bbcc53d039ffd62c7bfb7c150414d61369afe57e946" +dependencies = [ + "bumpalo", + "crc32fast", + "lockfree-object-pool", + "log", + "once_cell", + "simd-adler32", +] + [[package]] name = "zstd" version = "0.13.2" diff --git a/Cargo.toml b/Cargo.toml index d035d053..1023bee7 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -12,7 +12,7 @@ rust-version = "1.70.0" # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html [dependencies] -annonars = "0.41" +annonars = "0.42" anyhow = "1.0" async-compression = { version = "0.4", features = ["tokio", "gzip"] } aws-config = { version = "1.5", features = ["behavior-version-latest"] } @@ -35,11 +35,11 @@ ext-sort = { version = "0.1", features = ["memory-limit", "bytesize"] } fastrand = "2.2" flate2 = "1.0" futures = "0.3.31" -hgvs = "0.17.3" +hgvs = "0.17.4" indexmap = { version = "2.7", features = ["serde"] } itertools = "0.13" log = "0.4" -mehari = "0.29.6" +mehari = "0.30.1" multimap = "0.10" pbjson = "0.7" pbjson-types = "0.7"