From d10d344b7fc1e2d0d44372bd8ba8c5890cc0ebac Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Wed, 20 Nov 2024 13:20:02 +0100 Subject: [PATCH] chore: bump dependency --- Cargo.lock | 1846 +++++++++++---------------- Cargo.toml | 14 +- src/algos/phenomizer.rs | 8 +- src/common.rs | 28 +- src/convert/mod.rs | 11 +- src/index.rs | 2 +- src/query/mod.rs | 29 +- src/server/run/hpo_genes.rs | 3 +- src/server/run/hpo_omims.rs | 5 +- src/server/run/hpo_sim/term_gene.rs | 10 +- src/server/run/hpo_sim/term_term.rs | 3 +- src/server/run/hpo_terms.rs | 25 +- src/server/run/mod.rs | 11 +- 13 files changed, 799 insertions(+), 1196 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 01cbe9c..5935597 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -4,11 +4,11 @@ version = 3 [[package]] name = "actix-codec" -version = "0.5.1" +version = "0.5.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "617a8268e3537fe1d8c9ead925fca49ef6400927ee7bc26750e90ecee14ce4b8" +checksum = "5f7b0a21988c1bf877cf4759ef5ddaac04c1c9fe808c9142ecb78ba97d97a28a" dependencies = [ - "bitflags 1.3.2", + "bitflags", "bytes", "futures-core", "futures-sink", @@ -30,17 +30,17 @@ dependencies = [ "actix-service", "actix-utils", "ahash", - "base64 0.22.1", - "bitflags 2.4.1", + "base64", + "bitflags", "brotli", "bytes", "bytestring", - "derive_more", + "derive_more 0.99.18", "encoding_rs", "flate2", "futures-core", "h2", - "http 0.2.11", + "http", "httparse", "httpdate", "itoa", @@ -55,7 +55,7 @@ dependencies = [ "tokio", "tokio-util", "tracing", - "zstd 0.13.0", + "zstd", ] [[package]] @@ -76,7 +76,7 @@ checksum = "13d324164c51f63867b57e73ba5936ea151b8a41a1d23d1031eeb9f70d0236f8" dependencies = [ "bytestring", "cfg-if", - "http 0.2.11", + "http", "regex", "regex-lite", "serde", @@ -85,9 +85,9 @@ dependencies = [ [[package]] name = "actix-rt" -version = "2.9.0" +version = "2.10.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "28f32d40287d3f402ae0028a9d54bef51af15c8769492826a69d28f81893151d" +checksum = "24eda4e2a6e042aa4e55ac438a2ae052d3b5da0ecf83d7411e1a368946925208" dependencies = [ "futures-core", "tokio", @@ -95,9 +95,9 @@ dependencies = [ [[package]] name = "actix-server" -version = "2.3.0" +version = "2.5.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "3eb13e7eef0423ea6eab0e59f6c72e7cb46d33691ad56a726b3cd07ddec2c2d4" +checksum = "7ca2549781d8dd6d75c40cf6b6051260a2cc2f3c62343d761a969a0640646894" dependencies = [ "actix-rt", "actix-service", @@ -151,7 +151,7 @@ dependencies = [ "bytestring", "cfg-if", "cookie", - "derive_more", + "derive_more 0.99.18", "encoding_rs", "futures-core", "futures-util", @@ -187,19 +187,13 @@ dependencies = [ [[package]] name = "addr2line" -version = "0.21.0" +version = "0.24.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8a30b2e23b9e17a9f90641c7ab1549cd9b44f296d3ccbf309d2863cfe398a0cb" +checksum = "dfbe277e56a376000877090da837660b4427aad530e3028d44e0bffe4f89a1c1" dependencies = [ "gimli", ] -[[package]] -name = "adler" -version = "1.0.2" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe" - [[package]] name = "adler2" version = "2.0.0" @@ -208,9 +202,9 @@ checksum = "512761e0bb2578dd7380c6baaa0f4ce03e84f95e960231d1dec8bf4d7d6e2627" [[package]] name = "ahash" -version = "0.8.6" +version = "0.8.11" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "91429305e9f0a25f6205c5b8e0d2db09e0708a7a6df0f42212bb56c32c8ac97a" +checksum = "e89da841a80418a9b391ebaea17f5c112ffaaa96f621d2c285b5174da76b9011" dependencies = [ "cfg-if", "getrandom", @@ -221,9 +215,9 @@ dependencies = [ [[package]] name = "aho-corasick" -version = "1.1.2" +version = "1.1.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b2969dcb958b36655471fc61f7e416fa76033bdd4bfed0678d8fee1e2d07a1f0" +checksum = "8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916" dependencies = [ "memchr", ] @@ -245,106 +239,85 @@ dependencies = [ [[package]] name = "allocator-api2" -version = "0.2.16" +version = "0.2.20" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "0942ffc6dcaadf03badf6e6a2d0228460359d5e34b57ccdc720b7382dfbd5ec5" +checksum = "45862d1c77f2228b9e10bc609d5bc203d86ebc9b87ad8d5d5167a6c9abf739d9" [[package]] name = "anstream" -version = "0.6.7" +version = "0.6.18" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4cd2405b3ac1faab2990b74d728624cd9fd115651fcecc7c2d8daf01376275ba" +checksum = "8acc5369981196006228e28809f761875c0327210a891e941f4c683b3a99529b" dependencies = [ "anstyle", "anstyle-parse", "anstyle-query", "anstyle-wincon", "colorchoice", + "is_terminal_polyfill", "utf8parse", ] [[package]] name = "anstyle" -version = "1.0.8" +version = 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source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1cd54b81ec8d6180e24654d0b371ad22fc3dd083b6ff8ba325b72e00c87660a7" +checksum = "2109dbce0e72be3ec00bed26e6a7479ca384ad226efdd66db8fa2e3a38c83125" dependencies = [ "anstyle", - "windows-sys 0.52.0", + "windows-sys 0.59.0", ] [[package]] name = "anyhow" -version = "1.0.86" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b3d1d046238990b9cf5bcde22a3fb3584ee5cf65fb2765f454ed428c7a0063da" - -[[package]] -name = "approx" -version = "0.5.1" +version = "1.0.93" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "cab112f0a86d568ea0e627cc1d6be74a1e9cd55214684db5561995f6dad897c6" -dependencies = [ - "num-traits", -] - -[[package]] -name = "aquamarine" -version = "0.1.12" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a941c39708478e8eea39243b5983f1c42d2717b3620ee91f4a52115fd02ac43f" -dependencies = [ - "itertools 0.9.0", - "proc-macro-error", - "proc-macro2", - "quote", - "syn 1.0.109", -] +checksum = "4c95c10ba0b00a02636238b814946408b1322d5ac4760326e6fb8ec956d85775" [[package]] name = "arbitrary" -version = "1.3.2" +version = "1.4.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7d5a26814d8dcb93b0e5a0ff3c6d80a8843bafb21b39e8e18a6f05471870e110" +checksum = "dde20b3d026af13f561bdd0f15edf01fc734f0dafcedbaf42bba506a9517f223" dependencies = [ "derive_arbitrary", ] [[package]] name = "arc-swap" -version = "1.6.0" +version = "1.7.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "bddcadddf5e9015d310179a59bb28c4d4b9920ad0f11e8e14dbadf654890c9a6" +checksum = "69f7f8c3906b62b754cd5326047894316021dcfe5a194c8ea52bdd94934a3457" [[package]] name = "async-trait" -version = "0.1.75" +version = "0.1.83" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "fdf6721fb0140e4f897002dd086c06f6c27775df19cfe1fccb21181a48fd2c98" +checksum = "721cae7de5c34fbb2acd27e21e6d2cf7b886dce0c27388d46c4e6c47ea4318dd" dependencies = [ "proc-macro2", "quote", @@ -353,31 +326,25 @@ dependencies = [ [[package]] name = "autocfg" -version = "1.1.0" +version = "1.4.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa" +checksum = "ace50bade8e6234aa140d9a2f552bbee1db4d353f69b8217bc503490fc1a9f26" [[package]] name = "backtrace" -version = "0.3.69" +version = "0.3.74" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2089b7e3f35b9dd2d0ed921ead4f6d318c27680d4a5bd167b3ee120edb105837" +checksum = "8d82cb332cdfaed17ae235a638438ac4d4839913cc2af585c3c6746e8f8bee1a" dependencies = [ "addr2line", - "cc", "cfg-if", "libc", - "miniz_oxide 0.7.1", + "miniz_oxide", "object", "rustc-demangle", + "windows-targets 0.52.6", ] -[[package]] -name = "base64" -version = "0.21.5" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "35636a1494ede3b646cc98f74f8e62c773a38a659ebc777a2cf26b9b74171df9" - [[package]] name = "base64" version = "0.22.1" @@ -386,21 +353,15 @@ checksum = "72b3254f16251a8381aa12e40e3c4d2f0199f8c6508fbecb9d91f575e0fbb8c6" [[package]] name = "bitflags" -version = "1.3.2" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a" - -[[package]] -name = "bitflags" -version = "2.4.1" +version = "2.6.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "327762f6e5a765692301e5bb513e0d9fef63be86bbc14528052b1cd3e6f03e07" +checksum = "b048fb63fd8b5923fc5aa7b340d8e156aec7ec02f0c78fa8a6ddc2613f6f71de" [[package]] name = "bitpacking" -version = "0.8.4" +version = "0.9.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a8c7d2ac73c167c06af4a5f37e6e59d84148d57ccbe4480b76f0273eefea82d7" +checksum = "4c1d3e2bfd8d06048a179f7b17afc3188effa10385e7b00dc65af6aae732ea92" dependencies = [ "crunchy", ] @@ -448,15 +409,9 @@ dependencies = [ [[package]] name = "bumpalo" -version = "3.14.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7f30e7476521f6f8af1a1c4c0b8cc94f0bee37d91763d0ca2665f299b6cd8aec" - -[[package]] -name = "bytemuck" -version = "1.14.0" +version = "3.16.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "374d28ec25809ee0e23827c2ab573d729e293f281dfe393500e7ad618baa61c6" +checksum = "79296716171880943b8470b5f8d03aa55eb2e645a4874bdbb28adb49162e012c" [[package]] name = "byteorder" @@ -466,9 +421,9 @@ checksum = "1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b" [[package]] name = "bytes" -version = "1.5.0" +version = "1.8.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a2bd12c1caf447e69cd4528f47f94d203fd2582878ecb9e9465484c4148a8223" +checksum = "9ac0150caa2ae65ca5bd83f25c7de183dea78d4d366469f148435e2acfbad0da" [[package]] name = "bytestring" @@ -481,19 +436,20 @@ dependencies = [ [[package]] name = "cc" -version = "1.0.83" +version = "1.2.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f1174fb0b6ec23863f8b971027804a42614e347eafb0a95bf0b12cdae21fc4d0" +checksum = "fd9de9f2205d5ef3fd67e685b0df337994ddd4495e2a28d185500d0e1edfea47" dependencies = [ "jobserver", "libc", + "shlex", ] [[package]] name = "census" -version = "0.4.1" +version = "0.4.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "0fafee10a5dd1cffcb5cc560e0d0df8803d7355a2b12272e3557dee57314cb6e" +checksum = "4f4c707c6a209cbe82d10abd08e1ea8995e9ea937d2550646e02798948992be0" [[package]] name = "cfg-if" @@ -503,9 +459,9 @@ checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd" [[package]] name = "chrono" -version = "0.4.31" +version = "0.4.38" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7f2c685bad3eb3d45a01354cedb7d5faa66194d1d58ba6e267a8de788f79db38" +checksum = "a21f936df1771bf62b77f047b726c4625ff2e8aa607c01ec06e5a05bd8463401" dependencies = [ "num-traits", "serde", @@ -513,9 +469,9 @@ dependencies = [ [[package]] name = "clap" -version = "4.5.19" +version = "4.5.21" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7be5744db7978a28d9df86a214130d106a89ce49644cbc4e3f0c22c3fba30615" +checksum = "fb3b4b9e5a7c7514dfa52869339ee98b3156b0bfb4e8a77c4ff4babb64b1604f" dependencies = [ "clap_builder", "clap_derive", @@ -523,9 +479,9 @@ dependencies = [ [[package]] name = "clap-verbosity-flag" -version = "2.2.2" +version = "2.2.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e099138e1807662ff75e2cebe4ae2287add879245574489f9b1588eb5e5564ed" +checksum = "34c77f67047557f62582784fd7482884697731b2932c7d37ced54bce2312e1e2" dependencies = [ "clap", "log", @@ -533,14 +489,14 @@ dependencies = [ [[package]] name = "clap_builder" -version = "4.5.19" +version = "4.5.21" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a5fbc17d3ef8278f55b282b2a2e75ae6f6c7d4bb70ed3d0382375104bfafdb4b" +checksum = "b17a95aa67cc7b5ebd32aa5370189aa0d79069ef1c64ce893bd30fb24bff20ec" dependencies = [ "anstream", "anstyle", "clap_lex", - "strsim 0.11.1", + "strsim", ] [[package]] @@ -557,15 +513,15 @@ dependencies = [ [[package]] name = "clap_lex" -version = "0.7.1" +version = "0.7.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4b82cf0babdbd58558212896d1a4272303a57bdb245c2bf1147185fb45640e70" +checksum = "afb84c814227b90d6895e01398aee0d8033c00e7466aca416fb6a8e0eb19d8a7" [[package]] name = "colorchoice" -version = "1.0.0" +version = "1.0.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "acbf1af155f9b9ef647e42cdc158db4b64a1b61f743629225fde6f3e0be2a7c7" +checksum = "5b63caa9aa9397e2d9480a9b13673856c78d8ac123288526c37d7839f2a86990" [[package]] name = "console" @@ -576,7 +532,7 @@ dependencies = [ "encode_unicode", "lazy_static", "libc", - "unicode-width", + "unicode-width 0.1.14", "windows-sys 0.52.0", ] @@ -586,6 +542,15 @@ version = "0.4.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "6245d59a3e82a7fc217c5828a6692dbc6dfb63a0c8c90495621f7b9d79704a0e" +[[package]] +name = "convert_case" +version = "0.6.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "ec182b0ca2f35d8fc196cf3404988fd8b8c739a4d270ff118a398feb0cbec1ca" +dependencies = [ + "unicode-segmentation", +] + [[package]] name = "cookie" version = "0.16.2" @@ -599,9 +564,9 @@ dependencies = [ [[package]] name = "cpufeatures" -version = "0.2.11" +version = "0.2.15" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ce420fe07aecd3e67c5f910618fe65e94158f6dcc0adf44e00d69ce2bdfe0fd0" +checksum = "0ca741a962e1b0bff6d724a1a0958b686406e853bb14061f218562e1896f95e6" dependencies = [ "libc", ] @@ -617,35 +582,30 @@ dependencies = [ [[package]] name = "crossbeam-channel" -version = "0.5.9" +version = "0.5.13" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "14c3242926edf34aec4ac3a77108ad4854bffaa2e4ddc1824124ce59231302d5" +checksum = "33480d6946193aa8033910124896ca395333cae7e2d1113d1fef6c3272217df2" dependencies = [ - "cfg-if", "crossbeam-utils", ] [[package]] name = "crossbeam-deque" -version = "0.8.4" +version = "0.8.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "fca89a0e215bab21874660c67903c5f143333cab1da83d041c7ded6053774751" +checksum = "613f8cc01fe9cf1a3eb3d7f488fd2fa8388403e97039e2f73692932e291a770d" dependencies = [ - "cfg-if", "crossbeam-epoch", "crossbeam-utils", ] [[package]] name = "crossbeam-epoch" -version = "0.9.16" +version = "0.9.18" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2d2fe95351b870527a5d09bf563ed3c97c0cffb87cf1c78a591bf48bb218d9aa" +checksum = "5b82ac4a3c2ca9c3460964f020e1402edd5753411d7737aa39c3714ad1b5420e" dependencies = [ - "autocfg", - "cfg-if", "crossbeam-utils", - "memoffset", ] [[package]] @@ -693,9 +653,9 @@ dependencies = [ [[package]] name = "darling" -version = "0.20.3" +version = "0.20.10" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "0209d94da627ab5605dcccf08bb18afa5009cfbef48d8a8b7d7bdbc79be25c5e" +checksum = "6f63b86c8a8826a49b8c21f08a2d07338eec8d900540f8630dc76284be802989" dependencies = [ "darling_core", "darling_macro", @@ -703,23 +663,23 @@ dependencies = [ [[package]] name = "darling_core" -version = "0.20.3" +version = "0.20.10" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "177e3443818124b357d8e76f53be906d60937f0d3a90773a664fa63fa253e621" +checksum = "95133861a8032aaea082871032f5815eb9e98cef03fa916ab4500513994df9e5" dependencies = [ "fnv", "ident_case", "proc-macro2", "quote", - "strsim 0.10.0", + "strsim", "syn 2.0.87", ] [[package]] name = "darling_macro" -version = "0.20.3" +version = "0.20.10" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "836a9bbc7ad63342d6d6e7b815ccab164bc77a2d95d84bc3117a8c0d5c98e2d5" +checksum = "d336a2a514f6ccccaa3e09b02d41d35330c07ddf03a62165fcec10bb561c7806" dependencies = [ "darling_core", "quote", @@ -728,9 +688,9 @@ dependencies = [ [[package]] name = "deranged" -version = "0.3.10" +version = "0.3.11" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8eb30d70a07a3b04884d2677f06bec33509dc67ca60d92949e5535352d3191dc" +checksum = "b42b6fa04a440b495c8b04d0e71b707c585f83cb9cb28cf8cd0d976c315e31b4" dependencies = [ "powerfmt", "serde", @@ -738,9 +698,9 @@ dependencies = [ [[package]] name = "derive_arbitrary" -version = "1.3.2" +version = "1.4.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = 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"quote", + "syn 2.0.87", + "unicode-xid", +] + [[package]] name = "digest" version = "0.10.7" @@ -804,15 +786,15 @@ dependencies = [ [[package]] name = "downcast-rs" -version = "1.2.0" +version = "1.2.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "9ea835d29036a4087793836fa931b08837ad5e957da9e23886b29586fb9b6650" +checksum = "75b325c5dbd37f80359721ad39aca5a29fb04c89279657cffdda8736d0c0b9d2" [[package]] name = "either" -version = "1.9.0" +version = "1.13.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a26ae43d7bcc3b814de94796a5e736d4029efb0ee900c12e2d54c993ad1a1e07" +checksum = "60b1af1c220855b6ceac025d3f6ecdd2b7c4894bfe9cd9bda4fbb4bc7c0d4cf0" [[package]] name = "encode_unicode" @@ -822,24 +804,34 @@ checksum = "a357d28ed41a50f9c765dbfe56cbc04a64e53e5fc58ba79fbc34c10ef3df831f" [[package]] name = "encoding_rs" -version = "0.8.33" +version = "0.8.35" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7268b386296a025e474d5140678f75d6de9493ae55a5d709eeb9dd08149945e1" +checksum = "75030f3c4f45dafd7586dd6780965a8c7e8e285a5ecb86713e63a79c5b2766f3" dependencies = [ "cfg-if", ] +[[package]] +name = "env_filter" +version = "0.1.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "4f2c92ceda6ceec50f43169f9ee8424fe2db276791afde7b2cd8bc084cb376ab" +dependencies = [ + "log", + "regex", +] + [[package]] name = "env_logger" -version = "0.10.2" +version = "0.11.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4cd405aab171cb85d6735e5c8d9db038c17d3ca007a4d2c25f337935c3d90580" +checksum = "e13fa619b91fb2381732789fc5de83b45675e882f66623b7d8cb4f643017018d" dependencies = [ + "anstream", + "anstyle", + "env_filter", "humantime", - "is-terminal", "log", - "regex", - "termcolor", ] [[package]] @@ -850,9 +842,9 @@ checksum = "5443807d6dff69373d433ab9ef5378ad8df50ca6298caf15de6e52e24aaf54d5" [[package]] name = "errno" -version = "0.3.8" 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"file_diff" @@ -924,12 +916,12 @@ checksum = "0ce7134b9999ecaf8bcd65542e436736ef32ddca1b3e06094cb6ec5755203b80" [[package]] name = "flate2" -version = "1.0.33" +version = "1.0.35" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "324a1be68054ef05ad64b861cc9eaf1d623d2d8cb25b4bf2cb9cdd902b4bf253" +checksum = "c936bfdafb507ebbf50b8074c54fa31c5be9a1e7e5f467dd659697041407d07c" dependencies = [ "crc32fast", - "miniz_oxide 0.8.0", + "miniz_oxide", ] [[package]] @@ -938,6 +930,12 @@ version = "1.0.7" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "3f9eec918d3f24069decb9af1554cad7c880e2da24a9afd88aca000531ab82c1" +[[package]] +name = "foldhash" +version = "0.1.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "f81ec6369c545a7d40e4589b5597581fa1c441fe1cce96dd1de43159910a36a2" + [[package]] name = "form_urlencoded" version = "1.2.1" @@ -949,12 +947,12 @@ dependencies = [ [[package]] name = "fs4" -version = 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"f1bf18183cf54e8d6059647fc3063646a1801cf30896933ec2311622cc4b9a27" dependencies = [ "lock_api", "parking_lot_core", @@ -1872,22 +1746,22 @@ dependencies = [ [[package]] name = "parking_lot_core" -version = "0.9.9" +version = "0.9.10" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4c42a9226546d68acdd9c0a280d17ce19bfe27a46bf68784e4066115788d008e" +checksum = "1e401f977ab385c9e4e3ab30627d6f26d00e2c73eef317493c4ec6d468726cf8" dependencies = [ "cfg-if", "libc", "redox_syscall", "smallvec", - "windows-targets 0.48.5", + "windows-targets 0.52.6", ] [[package]] name = "paste" -version = "1.0.14" +version = "1.0.15" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "de3145af08024dea9fa9914f381a17b8fc6034dfb00f3a84013f7ff43f29ed4c" +checksum = "57c0d7b74b563b49d38dae00a0c37d4d6de9b432382b2892f0574ddcae73fd0a" [[package]] name = "percent-encoding" @@ -1897,9 +1771,9 @@ checksum = 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"prettyplease" -version = "0.2.15" +version = "0.2.25" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ae005bd773ab59b4725093fd7df83fd7892f7d8eafb48dbd7de6e024e4215f9d" +checksum = "64d1ec885c64d0457d564db4ec299b2dae3f9c02808b8ad9c3a089c591b18033" dependencies = [ "proc-macro2", "syn 2.0.87", @@ -2025,35 +1882,11 @@ dependencies = [ "toml_edit", ] -[[package]] -name = "proc-macro-error" -version = "1.0.4" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "da25490ff9892aab3fcf7c36f08cfb902dd3e71ca0f9f9517bea02a73a5ce38c" -dependencies = [ - "proc-macro-error-attr", - "proc-macro2", - "quote", - "syn 1.0.109", - "version_check", -] - -[[package]] -name = "proc-macro-error-attr" -version = "1.0.4" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a1be40180e52ecc98ad80b184934baf3d0d29f979574e439af5a55274b35f869" -dependencies = [ - "proc-macro2", - "quote", - "version_check", -] - [[package]] name = "proc-macro2" -version = "1.0.86" +version = "1.0.89" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "5e719e8df665df0d1c8fbfd238015744736151d4445ec0836b8e628aae103b77" +checksum = "f139b0662de085916d1fb67d2b4169d1addddda1919e696f3252b740b629986e" dependencies = [ "unicode-ident", ] @@ -2111,53 +1944,6 @@ dependencies = [ "prost", ] -[[package]] -name = "quinn" -version = "0.11.2" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e4ceeeeabace7857413798eb1ffa1e9c905a9946a57d81fb69b4b71c4d8eb3ad" -dependencies = [ - "bytes", - "pin-project-lite", - "quinn-proto", - "quinn-udp", - "rustc-hash", - "rustls", - "thiserror 1.0.69", - "tokio", - "tracing", -] - -[[package]] -name = "quinn-proto" -version = "0.11.3" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ddf517c03a109db8100448a4be38d498df8a210a99fe0e1b9eaf39e78c640efe" -dependencies = [ - "bytes", - "rand 0.8.5", - "ring", - "rustc-hash", - 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@@ -2253,9 +2033,9 @@ dependencies = [ [[package]] name = "rayon-core" -version = "1.12.0" +version = "1.12.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "5ce3fb6ad83f861aac485e76e1985cd109d9a3713802152be56c3b1f0e0658ed" +checksum = "1465873a3dfdaa8ae7cb14b4383657caab0b3e8a0aa9ae8e04b044854c8dfce2" dependencies = [ "crossbeam-deque", "crossbeam-utils", @@ -2272,18 +2052,18 @@ dependencies = [ [[package]] name = "redox_syscall" -version = "0.4.1" +version = "0.5.7" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4722d768eff46b75989dd134e5c353f0d6296e5aaa3132e776cbdb56be7731aa" +checksum = "9b6dfecf2c74bce2466cabf93f6664d6998a69eb21e39f4207930065b27b771f" dependencies = [ - "bitflags 1.3.2", + "bitflags", ] [[package]] name = "redox_users" -version = "0.4.4" +version = "0.4.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a18479200779601e498ada4e8c1e1f50e3ee19deb0259c25825a98b5603b2cb4" +checksum = "ba009ff324d1fc1b900bd1fdb31564febe58a8ccc8a6fdbb93b543d33b13ca43" dependencies = [ "getrandom", "libredox", @@ -2298,28 +2078,19 @@ checksum = "b544ef1b4eac5dc2db33ea63606ae9ffcfac26c1416a2806ae0bf5f56b201191" dependencies = [ "aho-corasick", "memchr", - "regex-automata 0.4.8", - "regex-syntax 0.8.5", -] - -[[package]] -name = "regex-automata" -version = "0.1.10" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "6c230d73fb8d8c1b9c0b3135c5142a8acee3a0558fb8db5cf1cb65f8d7862132" -dependencies = [ - "regex-syntax 0.6.29", + "regex-automata", + "regex-syntax", ] [[package]] name = "regex-automata" -version = "0.4.8" +version = "0.4.9" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "368758f23274712b504848e9d5a6f010445cc8b87a7cdb4d7cbee666c1288da3" +checksum = "809e8dc61f6de73b46c85f4c96486310fe304c434cfa43669d7b40f711150908" dependencies = [ "aho-corasick", "memchr", - "regex-syntax 0.8.5", + "regex-syntax", ] [[package]] @@ -2328,12 +2099,6 @@ version = "0.1.6" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "53a49587ad06b26609c52e423de037e7f57f20d53535d66e08c695f347df952a" -[[package]] -name = "regex-syntax" -version = "0.6.29" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f162c6dd7b008981e4d40210aca20b4bd0f9b60ca9271061b07f78537722f2e1" - [[package]] name = "regex-syntax" version = "0.8.5" @@ -2355,64 +2120,6 @@ dependencies = [ "winapi", ] -[[package]] -name = "reqwest" -version = "0.12.5" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c7d6d2a27d57148378eb5e111173f4276ad26340ecc5c49a4a2152167a2d6a37" -dependencies = [ - "base64 0.22.1", - "bytes", - "futures-channel", - "futures-core", - "futures-util", - "http 1.1.0", - "http-body", - "http-body-util", - "hyper", - "hyper-rustls", - "hyper-util", - "ipnet", - "js-sys", - "log", - "mime", - "once_cell", - "percent-encoding", - "pin-project-lite", - "quinn", - "rustls", - "rustls-pemfile", - "rustls-pki-types", - "serde", - "serde_json", - "serde_urlencoded", - "sync_wrapper", - "tokio", - "tokio-rustls", - "tower-service", - "url", - "wasm-bindgen", - "wasm-bindgen-futures", - "web-sys", - "webpki-roots", - "winreg", -] - -[[package]] -name = "ring" -version = "0.17.8" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c17fa4cb658e3583423e915b9f3acc01cceaee1860e33d59ebae66adc3a2dc0d" -dependencies = [ - "cc", - "cfg-if", - "getrandom", - "libc", - "spin", - "untrusted", - "windows-sys 0.52.0", -] - [[package]] name = "rstest" version = "0.23.0" @@ -2489,9 +2196,9 @@ dependencies = [ [[package]] name = "rustc-demangle" -version = "0.1.23" +version = "0.1.24" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d626bb9dae77e28219937af045c257c28bfd3f69333c512553507f5f9798cb76" +checksum = "719b953e2095829ee67db738b3bfa9fa368c94900df327b3f07fe6e794d2fe1f" [[package]] name = "rustc-hash" @@ -2510,78 +2217,28 @@ dependencies = [ [[package]] name = "rustix" -version = "0.38.28" +version = "0.38.41" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "72e572a5e8ca657d7366229cdde4bd14c4eb5499a9573d4d366fe1b599daa316" +checksum = "d7f649912bc1495e167a6edee79151c84b1bad49748cb4f1f1167f459f6224f6" dependencies = [ - "bitflags 2.4.1", + "bitflags", "errno", "libc", "linux-raw-sys", "windows-sys 0.52.0", ] -[[package]] -name = "rustls" -version = "0.23.11" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4828ea528154ae444e5a642dbb7d5623354030dc9822b83fd9bb79683c7399d0" -dependencies = [ - "once_cell", - "ring", - "rustls-pki-types", - "rustls-webpki", - "subtle", - "zeroize", -] - -[[package]] -name = "rustls-pemfile" -version = "2.1.2" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "29993a25686778eb88d4189742cd713c9bce943bc54251a33509dc63cbacf73d" -dependencies = [ - "base64 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- -[[package]] -name = "safe_arch" -version = "0.7.1" +version = "1.0.18" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f398075ce1e6a179b46f51bd88d0598b92b00d3551f1a2d4ac49e771b56ac354" -dependencies = [ - "bytemuck", -] +checksum = "f3cb5ba0dc43242ce17de99c180e96db90b235b8a9fdc9543c96d2209116bd9f" [[package]] name = "same-file" @@ -2592,12 +2249,6 @@ dependencies = [ "winapi-util", ] -[[package]] -name = "scoped-tls" -version = "1.0.1" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e1cf6437eb19a8f4a6cc0f7dca544973b0b78843adbfeb3683d1a94a0024a294" - [[package]] name = "scopeguard" version = "1.2.0" @@ -2606,24 +2257,24 @@ checksum = "94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49" [[package]] name = "semver" -version = "1.0.20" +version = "1.0.23" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "836fa6a3e1e547f9a2c4040802ec865b5d85f4014efe00555d7090a3dcaa1090" +checksum = 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= "c7fceb2473b9166b2294ef05efcb65a3db80803f0b03ef86a5fc88a2b85ee377" dependencies = [ "itoa", "memchr", @@ -2665,11 +2316,11 @@ dependencies = [ [[package]] name = "serde_with" -version = "3.9.0" +version = "3.11.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "69cecfa94848272156ea67b2b1a53f20fc7bc638c4a46d2f8abde08f05f4b857" +checksum = "8e28bdad6db2b8340e449f7108f020b3b092e8583a9e3fb82713e1d4e71fe817" dependencies = [ - "base64 0.22.1", + "base64", "chrono", "hex", "indexmap", @@ -2682,9 +2333,9 @@ dependencies = [ [[package]] name = "serde_with_macros" -version = "3.9.0" +version = "3.11.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a8fee4991ef4f274617a51ad4af30519438dacb2f56ac773b08a1922ff743350" +checksum = "9d846214a9854ef724f3da161b426242d8de7c1fc7de2f89bb1efcb154dca79d" dependencies = [ "darling", "proc-macro2", @@ -2694,9 +2345,9 @@ dependencies = [ [[package]] name = "serde_yaml" -version = "0.9.30" +version = 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"proc-macro2", + "quote", + "syn 2.0.87", +] [[package]] name = "tantivy" -version = "0.21.1" +version = "0.22.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d6083cd777fa94271b8ce0fe4533772cb8110c3044bab048d20f70108329a1f2" +checksum = "f8d0582f186c0a6d55655d24543f15e43607299425c5ad8352c242b914b31856" dependencies = [ "aho-corasick", "arc-swap", - "async-trait", - "base64 0.21.5", + "base64", "bitpacking", "byteorder", "census", @@ -2934,16 +2557,16 @@ dependencies = [ "crossbeam-channel", "downcast-rs", "fastdivide", + "fnv", "fs4", "htmlescape", - "itertools 0.11.0", + "itertools 0.12.1", "levenshtein_automata", "log", "lru", "lz4_flex", "measure_time", "memmap2", - "murmurhash32", "num_cpus", "once_cell", "oneshot", @@ -2971,22 +2594,22 @@ dependencies = [ [[package]] name = "tantivy-bitpacker" -version = "0.5.0" +version = "0.6.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = 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[[package]] @@ -3735,17 +3272,18 @@ dependencies = [ [[package]] name = "windows-targets" -version = "0.52.0" +version = "0.52.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8a18201040b24831fbb9e4eb208f8892e1f50a37feb53cc7ff887feb8f50e7cd" +checksum = "9b724f72796e036ab90c1021d4780d4d3d648aca59e491e6b98e725b84e99973" dependencies = [ - "windows_aarch64_gnullvm 0.52.0", - "windows_aarch64_msvc 0.52.0", - "windows_i686_gnu 0.52.0", - "windows_i686_msvc 0.52.0", - "windows_x86_64_gnu 0.52.0", - "windows_x86_64_gnullvm 0.52.0", - "windows_x86_64_msvc 0.52.0", + "windows_aarch64_gnullvm 0.52.6", + "windows_aarch64_msvc 0.52.6", + "windows_i686_gnu 0.52.6", + "windows_i686_gnullvm", + "windows_i686_msvc 0.52.6", + "windows_x86_64_gnu 0.52.6", + "windows_x86_64_gnullvm 0.52.6", + "windows_x86_64_msvc 0.52.6", ] [[package]] @@ -3756,9 +3294,9 @@ checksum = "2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8" [[package]] name = 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[[package]] -name = "zeroize" -version = "1.8.1" +name = "zerovec-derive" +version = "0.10.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ced3678a2879b30306d323f4542626697a464a97c0a07c9aebf7ebca65cd4dde" +checksum = "6eafa6dfb17584ea3e2bd6e76e0cc15ad7af12b09abdd1ca55961bed9b1063c6" +dependencies = [ + "proc-macro2", + "quote", + "syn 2.0.87", +] [[package]] name = "zip" -version = "1.1.4" +version = "2.2.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "9cc23c04387f4da0374be4533ad1208cbb091d5c11d070dfef13676ad6497164" +checksum = "dc5e4288ea4057ae23afc69a4472434a87a2495cafce6632fd1c4ec9f5cf3494" dependencies = [ "arbitrary", "crc32fast", @@ -3889,52 +3497,48 @@ dependencies = [ "displaydoc", "flate2", "indexmap", - "num_enum", + "memchr", "thiserror 1.0.69", + "zopfli", ] [[package]] -name = "zstd" -version = "0.12.4" +name = "zopfli" +version = "0.8.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1a27595e173641171fc74a1232b7b1c7a7cb6e18222c11e9dfb9888fa424c53c" +checksum = "e5019f391bac5cf252e93bbcc53d039ffd62c7bfb7c150414d61369afe57e946" dependencies = [ - "zstd-safe 6.0.6", + "bumpalo", + "crc32fast", + "lockfree-object-pool", + "log", + "once_cell", + "simd-adler32", ] [[package]] name = "zstd" -version = "0.13.0" +version = "0.13.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "bffb3309596d527cfcba7dfc6ed6052f1d39dfbd7c867aa2e865e4a449c10110" +checksum = "fcf2b778a664581e31e389454a7072dab1647606d44f7feea22cd5abb9c9f3f9" dependencies = [ - "zstd-safe 7.0.0", -] - -[[package]] -name = "zstd-safe" -version = "6.0.6" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ee98ffd0b48ee95e6c5168188e44a54550b1564d9d530ee21d5f0eaed1069581" -dependencies = [ - "libc", - "zstd-sys", + "zstd-safe", ] [[package]] name = "zstd-safe" -version = "7.0.0" +version = "7.2.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "43747c7422e2924c11144d5229878b98180ef8b06cca4ab5af37afc8a8d8ea3e" +checksum = "54a3ab4db68cea366acc5c897c7b4d4d1b8994a9cd6e6f841f8964566a419059" dependencies = [ "zstd-sys", ] [[package]] name = "zstd-sys" -version = "2.0.9+zstd.1.5.5" +version = "2.0.13+zstd.1.5.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "9e16efa8a874a0481a574084d34cc26fdb3b99627480f785888deb6386506656" +checksum = "38ff0f21cfee8f97d94cef41359e0c89aa6113028ab0291aa8ca0038995a95aa" dependencies = [ "cc", "pkg-config", diff --git a/Cargo.toml b/Cargo.toml index 58a576b..5e4c81c 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -15,12 +15,12 @@ clap-verbosity-flag = "2.2" clap = { version = "4.5", features = ["derive", "help", "env"] } console = "0.15" csv = "1.3" -derive_more = "0.99" -env_logger = "0.10" +derive_more = { version = "1.0", features = ["full"] } +env_logger = "0.11" fastobo = "0.15.2" fastrand = "2.1" flate2 = "1.0" -hpo = "0.8" +hpo = "0.11" indexmap = { version = "2.6", features = ["serde"] } indicatif = { version = "0.17", features = ["rayon"] } itertools = "0.13" @@ -36,13 +36,13 @@ serde_with = { version = "3.9", features=["alloc", "macros", "indexmap_2"], defa shellexpand = "3.0" strum_macros = "0.26" strum = { version = "0.26", features = ["strum_macros", "derive"] } -tantivy = "0.21.1" -tempdir = "0.3.7" +tantivy = "0.22" +tempdir = "0.3" thiserror = "2.0" tracing = "0.1" tracing-subscriber = "0.3" -utoipa-swagger-ui = { version = "7.1.0", features = ["actix-web"] } -utoipa = { version = "4.2", features = ["actix_extras", "chrono", "indexmap", "preserve_order", "yaml"] } +utoipa-swagger-ui = { version = "8.0", features = ["actix-web"] } +utoipa = { version = "5.2", features = ["actix_extras", "chrono", "indexmap", "preserve_order", "yaml"] } [build-dependencies] anyhow = "1.0" diff --git a/src/algos/phenomizer.rs b/src/algos/phenomizer.rs index cd49f04..c2d16c8 100644 --- a/src/algos/phenomizer.rs +++ b/src/algos/phenomizer.rs @@ -47,7 +47,11 @@ fn score_dir(qs: &HpoGroup, ds: &HpoGroup, o: &Ontology, s: &impl Similarity) -> #[cfg(test)] mod test { use super::*; - use hpo::{annotations::OmimDiseaseId, term::HpoGroup, HpoTermId, Ontology}; + use hpo::{ + annotations::{Disease as _, OmimDiseaseId}, + term::HpoGroup, + HpoTermId, Ontology, + }; fn load_hpo() -> Result { Ok(Ontology::from_standard("tests/data/hpo")?) @@ -84,7 +88,7 @@ mod test { let score = score(&prepare(query), &hpo_marfan, &hpo); - assert!((score - 1.757_194).abs() < 0.00001, "score = {score}"); + assert!((score - 1.756_347).abs() < 0.00001, "score = {score}"); Ok(()) } diff --git a/src/common.rs b/src/common.rs index 05539b4..891e5b7 100644 --- a/src/common.rs +++ b/src/common.rs @@ -66,10 +66,10 @@ pub fn load_hpo>(path: P) -> Result for StandardCombiner { match val { ScoreCombiner::FunSimAvg => StandardCombiner::FunSimAvg, ScoreCombiner::FunSimMax => StandardCombiner::FunSimMax, - ScoreCombiner::Bma => StandardCombiner::Bwa, + ScoreCombiner::Bma => StandardCombiner::Bma, } } } diff --git a/src/convert/mod.rs b/src/convert/mod.rs index 4abd108..0be185a 100644 --- a/src/convert/mod.rs +++ b/src/convert/mod.rs @@ -29,14 +29,9 @@ pub fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), anyhow: tracing::info!("args_common = {:?}", &args_common); tracing::info!("args = {:?}", &args); - if let Some(level) = args_common.verbose.log_level() { - match level { - log::Level::Trace | log::Level::Debug => { - std::env::set_var("RUST_LOG", "debug"); - env_logger::init_from_env(env_logger::Env::new().default_filter_or("info")); - } - _ => (), - } + if let Some(log::Level::Trace | log::Level::Debug) = args_common.verbose.log_level() { + std::env::set_var("RUST_LOG", "debug"); + env_logger::init_from_env(env_logger::Env::new().default_filter_or("info")); } tracing::info!("Loading HPO..."); diff --git a/src/index.rs b/src/index.rs index b23683c..d386331 100644 --- a/src/index.rs +++ b/src/index.rs @@ -98,7 +98,7 @@ impl Index { .iter() .filter_map(fastobo::ast::EntityFrame::as_term) { - let mut doc = tantivy::Document::default(); + let mut doc = tantivy::TantivyDocument::default(); doc.add_field_value( schema.get_field("term_id")?, diff --git a/src/query/mod.rs b/src/query/mod.rs index 59ab314..c83e0d3 100644 --- a/src/query/mod.rs +++ b/src/query/mod.rs @@ -52,7 +52,15 @@ pub mod query_result { /// Struct for storing gene information in the result. #[derive( - serde::Serialize, serde::Deserialize, PartialEq, Eq, PartialOrd, Ord, Debug, Clone, + PartialEq, + Eq, + PartialOrd, + Ord, + Debug, + Clone, + serde::Serialize, + serde::Deserialize, + utoipa::ToSchema, )] #[serde_with::skip_serializing_none] pub struct Gene { @@ -65,7 +73,7 @@ pub mod query_result { } /// The performed query. - #[derive(serde::Serialize, serde::Deserialize, utoipa::ToSchema, Debug, Clone)] + #[derive(Debug, Clone, serde::Serialize, serde::Deserialize, utoipa::ToSchema)] #[schema(title = "HpoSimTermGeneQuery")] pub struct Query { /// The query HPO terms. @@ -75,7 +83,7 @@ pub mod query_result { } /// Result container data structure. - #[derive(serde::Serialize, serde::Deserialize, utoipa::ToSchema, Debug, Clone)] + #[derive(Debug, Clone, serde::Serialize, serde::Deserialize, utoipa::ToSchema)] #[schema(title = "HpoSimTermGeneResult")] pub struct Result { /// Version information. @@ -87,7 +95,7 @@ pub mod query_result { } /// Store score for a record with information on individual terms. - #[derive(serde::Serialize, serde::Deserialize, utoipa::ToSchema, Debug, Clone)] + #[derive(Debug, Clone, serde::Serialize, serde::Deserialize, utoipa::ToSchema)] #[schema(title = "HpoSimTermGeneResultEntry")] pub struct ResultEntry { /// The gene symbol. @@ -100,7 +108,7 @@ pub mod query_result { } /// Detailed term scores. - #[derive(serde::Serialize, serde::Deserialize, utoipa::ToSchema, Debug, Clone)] + #[derive(Debug, Clone, serde::Serialize, serde::Deserialize, utoipa::ToSchema)] #[schema(title = "HpoSimTermGeneTermDetails")] pub struct TermDetails { /// The query HPO term. @@ -258,14 +266,9 @@ pub fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), anyhow: tracing::info!("args_common = {:?}", &args_common); tracing::info!("args = {:?}", &args); - if let Some(level) = args_common.verbose.log_level() { - match level { - log::Level::Trace | log::Level::Debug => { - std::env::set_var("RUST_LOG", "debug"); - env_logger::init_from_env(env_logger::Env::new().default_filter_or("info")); - } - _ => (), - } + if let Some(log::Level::Trace | log::Level::Debug) = args_common.verbose.log_level() { + std::env::set_var("RUST_LOG", "debug"); + env_logger::init_from_env(env_logger::Env::new().default_filter_or("info")); } tracing::info!("Loading HPO..."); diff --git a/src/server/run/hpo_genes.rs b/src/server/run/hpo_genes.rs index 40ac46f..a8bbdf5 100644 --- a/src/server/run/hpo_genes.rs +++ b/src/server/run/hpo_genes.rs @@ -5,7 +5,6 @@ use std::{collections::HashMap, sync::Arc}; use actix_web::{ get, web::{self, Data, Json, Path}, - Responder, }; use hpo::{ annotations::{AnnotationId, Gene, GeneId}, @@ -143,7 +142,7 @@ async fn handle( data: Data>, _path: Path<()>, query: web::Query, -) -> actix_web::Result { +) -> actix_web::Result, CustomError> { let ontology = &data.ontology; let match_ = query.match_.unwrap_or_default(); let mut result: Vec = Vec::new(); diff --git a/src/server/run/hpo_omims.rs b/src/server/run/hpo_omims.rs index 9d50b59..f2c35cf 100644 --- a/src/server/run/hpo_omims.rs +++ b/src/server/run/hpo_omims.rs @@ -5,10 +5,9 @@ use std::sync::Arc; use actix_web::{ get, web::{self, Data, Json, Path}, - Responder, }; use hpo::{ - annotations::{OmimDisease, OmimDiseaseId}, + annotations::{Disease as _, OmimDisease, OmimDiseaseId}, term::HpoGroup, Ontology, }; @@ -178,7 +177,7 @@ async fn handle( data: Data>, _path: Path<()>, query: web::Query, -) -> actix_web::Result { +) -> actix_web::Result, CustomError> { let ontology = &data.ontology; let match_ = query.match_.unwrap_or_default(); let mut result: Vec = Vec::new(); diff --git a/src/server/run/hpo_sim/term_gene.rs b/src/server/run/hpo_sim/term_gene.rs index f523d2b..ccdf78e 100644 --- a/src/server/run/hpo_sim/term_gene.rs +++ b/src/server/run/hpo_sim/term_gene.rs @@ -6,13 +6,15 @@ use std::sync::Arc; use actix_web::{ get, web::{self, Data, Json, Path}, - Responder, }; use hpo::{annotations::GeneId, term::HpoGroup, HpoTermId, Ontology}; use super::super::CustomError; -use crate::{query, server::run::WebServerData}; +use crate::{ + query::{self, query_result}, + server::run::WebServerData, +}; /// Parameters for `handle`. /// @@ -52,7 +54,7 @@ pub struct Query { operation_id = "hpo_sim_term_gene", params(Query), responses( - (status = 200, description = "The query was successful.", body = Result), + (status = 200, description = "The query was successful.", body = query_result::Result), ) )] #[get("/hpo/sim/term-gene")] @@ -60,7 +62,7 @@ async fn handle( data: Data>, _path: Path<()>, query: web::Query, -) -> actix_web::Result { +) -> actix_web::Result, CustomError> { let hpo: &Ontology = &data.ontology; // Translate strings from the query into an `HpoGroup`. diff --git a/src/server/run/hpo_sim/term_term.rs b/src/server/run/hpo_sim/term_term.rs index 39e0d5a..1f572a1 100644 --- a/src/server/run/hpo_sim/term_term.rs +++ b/src/server/run/hpo_sim/term_term.rs @@ -6,7 +6,6 @@ use std::sync::Arc; use actix_web::{ get, web::{self, Data, Json, Path}, - Responder, }; use hpo::{ similarity::{Builtins, Similarity}, @@ -116,7 +115,7 @@ async fn handle( data: Data>, _path: Path<()>, query: web::Query, -) -> actix_web::Result { +) -> actix_web::Result, CustomError> { let ontology: &Ontology = &data.ontology; let mut result = Vec::new(); diff --git a/src/server/run/hpo_terms.rs b/src/server/run/hpo_terms.rs index 339bf00..0b92750 100644 --- a/src/server/run/hpo_terms.rs +++ b/src/server/run/hpo_terms.rs @@ -5,9 +5,9 @@ use std::{collections::HashMap, sync::Arc}; use actix_web::{ get, web::{self, Data, Json, Path}, - Responder, }; use hpo::{annotations::AnnotationId, HpoTerm, HpoTermId, Ontology}; +use tantivy::schema::Value as _; use crate::{common::Version, server::run::WebServerData}; @@ -105,7 +105,7 @@ impl ResultEntry { genes: bool, ncbi_to_hgnc: &HashMap, index: &crate::index::Index, - doc: Option<&tantivy::Document>, + doc: Option<&tantivy::TantivyDocument>, ) -> Result { let field_term_id = index .schema() @@ -147,12 +147,12 @@ impl ResultEntry { let definition = doc .get_all(field_def) - .filter_map(|f| f.as_text().map(std::string::ToString::to_string)) + .filter_map(|f| f.as_value().as_str().map(std::string::ToString::to_string)) .collect::>(); let definition = definition.first().cloned(); let synonyms = doc .get_all(field_synonym) - .filter_map(|f| f.as_text().map(std::string::ToString::to_string)) + .filter_map(|f| f.as_value().as_str().map(std::string::ToString::to_string)) .collect::>(); let synonyms = if synonyms.is_empty() { None @@ -161,7 +161,7 @@ impl ResultEntry { }; let xrefs = doc .get_all(field_xref) - .filter_map(|f| f.as_text().map(std::string::ToString::to_string)) + .filter_map(|f| f.as_value().as_str().map(std::string::ToString::to_string)) .collect::>(); let xrefs = if xrefs.is_empty() { None } else { Some(xrefs) }; @@ -215,7 +215,7 @@ pub struct Result_ { operation_id = "hpo_terms", params(Query), responses( - (status = 200, description = "The query was successful.", body = Result), + (status = 200, description = "The query was successful.", body = Result_), ) )] #[get("/hpo/terms")] @@ -223,7 +223,7 @@ async fn handle( data: Data>, _path: Path<()>, query: web::Query, -) -> actix_web::Result { +) -> actix_web::Result, CustomError> { let ontology = &data.ontology; let mut result: Vec = Vec::new(); @@ -326,15 +326,18 @@ async fn handle( .map_err(|e| CustomError::new(anyhow::anyhow!("Error searching index: {}", e)))?; for (_score, doc_address) in top_docs { - let retrieved_doc = searcher.doc(doc_address).map_err(|e| { - CustomError::new(anyhow::anyhow!("Error retrieving document: {}", e)) - })?; + let retrieved_doc = searcher + .doc::(doc_address) + .map_err(|e| { + CustomError::new(anyhow::anyhow!("Error retrieving document: {}", e)) + })?; let term_id = retrieved_doc .get_first(field_term_id) .ok_or_else(|| { CustomError::new(anyhow::anyhow!("Document has no `term_id` field")) })? - .as_text() + .as_value() + .as_str() .unwrap_or_default(); let term_id = HpoTermId::from(term_id.to_string()); let term = ontology.hpo(term_id).ok_or_else(|| { diff --git a/src/server/run/mod.rs b/src/server/run/mod.rs index a464c92..2885121 100644 --- a/src/server/run/mod.rs +++ b/src/server/run/mod.rs @@ -245,14 +245,9 @@ pub fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), anyhow: tracing::info!("args_common = {:?}", &args_common); tracing::info!("args = {:?}", &args); - if let Some(level) = args_common.verbose.log_level() { - match level { - log::Level::Trace | log::Level::Debug => { - std::env::set_var("RUST_LOG", "debug"); - env_logger::init_from_env(env_logger::Env::new().default_filter_or("info")); - } - _ => (), - } + if let Some(log::Level::Trace | log::Level::Debug) = args_common.verbose.log_level() { + std::env::set_var("RUST_LOG", "debug"); + env_logger::init_from_env(env_logger::Env::new().default_filter_or("info")); } // Load data that we need for running the server.