diff --git a/Cargo.lock b/Cargo.lock index e3b444e5..63836aa7 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -40,7 +40,7 @@ dependencies = [ "flate2", "futures-core", "h2", - "http", + "http 0.2.12", "httparse", "httpdate", "itoa", @@ -76,7 +76,7 @@ checksum = "13d324164c51f63867b57e73ba5936ea151b8a41a1d23d1031eeb9f70d0236f8" dependencies = [ "bytestring", "cfg-if", - "http", + "http 0.2.12", "regex", "regex-lite", "serde", @@ -290,6 +290,7 @@ dependencies = [ "serde", "serde_json", "serde_with", + "serde_yaml", "strum 0.26.3", "temp_testdir", "test-log", @@ -297,6 +298,8 @@ dependencies = [ "tracing", "tracing-subscriber", "tracing-test", + "utoipa", + "utoipa-swagger-ui", ] [[package]] @@ -363,6 +366,15 @@ dependencies = [ "num-traits", ] +[[package]] +name = "arbitrary" +version = "1.3.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "7d5a26814d8dcb93b0e5a0ff3c6d80a8843bafb21b39e8e18a6f05471870e110" +dependencies = [ + "derive_arbitrary", +] + [[package]] name = "autocfg" version = "1.3.0" @@ -909,6 +921,17 @@ dependencies = [ "syn 1.0.109", ] +[[package]] +name = "derive_arbitrary" +version = "1.3.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "67e77553c4162a157adbf834ebae5b415acbecbeafc7a74b0e886657506a7611" +dependencies = [ + "proc-macro2", + "quote", + "syn 2.0.66", +] + [[package]] name = "derive_more" version = "0.99.17" @@ -1237,7 +1260,7 @@ dependencies = [ "futures-core", "futures-sink", "futures-util", - "http", + "http 0.2.12", "indexmap", "slab", "tokio", @@ -1280,6 +1303,40 @@ dependencies = [ "itoa", ] +[[package]] +name = "http" +version = "1.1.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "21b9ddb458710bc376481b842f5da65cdf31522de232c1ca8146abce2a358258" +dependencies = [ + "bytes", + "fnv", + "itoa", +] + +[[package]] +name = "http-body" +version = "1.0.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "1efedce1fb8e6913f23e0c92de8e62cd5b772a67e7b3946df930a62566c93184" +dependencies = [ + "bytes", + "http 1.1.0", +] + +[[package]] +name = "http-body-util" +version = "0.1.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "793429d76616a256bcb62c2a2ec2bed781c8307e797e2598c50010f2bee2544f" +dependencies = [ + "bytes", + "futures-util", + "http 1.1.0", + "http-body", + "pin-project-lite", +] + [[package]] name = "httparse" version = "1.9.3" @@ -1298,6 +1355,63 @@ version = "2.1.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "9a3a5bfb195931eeb336b2a7b4d761daec841b97f947d34394601737a7bba5e4" +[[package]] +name = "hyper" +version = "1.4.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "50dfd22e0e76d0f662d429a5f80fcaf3855009297eab6a0a9f8543834744ba05" +dependencies = [ + "bytes", + "futures-channel", + "futures-util", + "http 1.1.0", + "http-body", + "httparse", + "itoa", + "pin-project-lite", + "smallvec", + "tokio", + "want", +] + +[[package]] +name = "hyper-rustls" +version = "0.27.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "5ee4be2c948921a1a5320b629c4193916ed787a7f7f293fd3f7f5a6c9de74155" +dependencies = [ + "futures-util", + "http 1.1.0", + "hyper", + "hyper-util", + "rustls", + "rustls-pki-types", + "tokio", + "tokio-rustls", + "tower-service", + "webpki-roots", +] + +[[package]] +name = "hyper-util" +version = "0.1.6" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "3ab92f4f49ee4fb4f997c784b7a2e0fa70050211e0b6a287f898c3c9785ca956" +dependencies = [ + "bytes", + "futures-channel", + "futures-util", + "http 1.1.0", + "http-body", + "hyper", + "pin-project-lite", + "socket2", + "tokio", + "tower", + "tower-service", + "tracing", +] + [[package]] name = "iana-time-zone" version = "0.1.60" @@ -1504,6 +1618,12 @@ dependencies = [ "cfg-if", ] +[[package]] +name = "ipnet" +version = "2.9.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "8f518f335dce6725a761382244631d86cf0ccb2863413590b31338feb467f9c3" + [[package]] name = "is_terminal_polyfill" version = "1.70.0" @@ -1720,6 +1840,16 @@ version = "0.3.17" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "6877bb514081ee2a7ff5ef9de3281f14a4dd4bceac4c09388074a6b5df8a139a" +[[package]] +name = "mime_guess" +version = "2.0.5" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "f7c44f8e672c00fe5308fa235f821cb4198414e1c77935c1ab6948d3fd78550e" +dependencies = [ + "mime", + "unicase", +] + [[package]] name = "minimal-lexical" version = "0.2.1" @@ -1971,6 +2101,27 @@ dependencies = [ "libm", ] +[[package]] +name = "num_enum" +version = "0.7.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "02339744ee7253741199f897151b38e72257d13802d4ee837285cc2990a90845" +dependencies = [ + "num_enum_derive", +] + +[[package]] +name = "num_enum_derive" +version = "0.7.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "681030a937600a36906c185595136d26abfebb4aa9c65701cefcaf8578bb982b" +dependencies = [ + "proc-macro-crate", + "proc-macro2", + "quote", + "syn 2.0.66", +] + [[package]] name = "number_prefix" version = "0.4.0" @@ -2089,6 +2240,26 @@ dependencies = [ "indexmap", ] +[[package]] +name = "pin-project" +version = "1.1.5" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "b6bf43b791c5b9e34c3d182969b4abb522f9343702850a2e57f460d00d09b4b3" +dependencies = [ + "pin-project-internal", +] + +[[package]] +name = "pin-project-internal" +version = "1.1.5" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "2f38a4412a78282e09a2cf38d195ea5420d15ba0602cb375210efbc877243965" +dependencies = [ + "proc-macro2", + "quote", + "syn 2.0.66", +] + [[package]] name = "pin-project-lite" version = "0.2.14" @@ -2154,6 +2325,30 @@ 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 = "1.0.85" @@ -2216,6 +2411,53 @@ 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 1.1.0", + "rustls", + "thiserror", + "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", + "ring", + "rustc-hash 1.1.0", + "rustls", + "slab", + "thiserror", + "tinyvec", + "tracing", +] + +[[package]] +name = "quinn-udp" +version = "0.5.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "9096629c45860fc7fb143e125eb826b5e721e10be3263160c7d60ca832cf8c46" +dependencies = [ + "libc", + "once_cell", + "socket2", + "tracing", + "windows-sys 0.52.0", +] + [[package]] name = "quote" version = "1.0.36" @@ -2356,6 +2598,64 @@ version = "1.9.3" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "ba39f3699c378cd8970968dcbff9c43159ea4cfbd88d43c00b22f2ef10a435d2" +[[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 = "rocksdb" version = "0.22.0" @@ -2407,6 +2707,40 @@ dependencies = [ "unicode-ident", ] +[[package]] +name = "rust-embed" +version = "8.5.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "fa66af4a4fdd5e7ebc276f115e895611a34739a9c1c01028383d612d550953c0" +dependencies = [ + "rust-embed-impl", + "rust-embed-utils", + "walkdir", +] + +[[package]] +name = "rust-embed-impl" +version = "8.5.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "6125dbc8867951125eec87294137f4e9c2c96566e61bf72c45095a7c77761478" +dependencies = [ + "proc-macro2", + "quote", + "rust-embed-utils", + "syn 2.0.66", + "walkdir", +] + +[[package]] +name = "rust-embed-utils" +version = "8.5.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "2e5347777e9aacb56039b0e1f28785929a8a3b709e87482e7442c72e7c12529d" +dependencies = [ + "sha2", + "walkdir", +] + [[package]] name = "rustc-demangle" version = "0.1.24" @@ -2456,6 +2790,47 @@ dependencies = [ "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 0.22.1", + "rustls-pki-types", +] + +[[package]] +name = "rustls-pki-types" +version = "1.7.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "976295e77ce332211c0d24d92c0e83e50f5c5f046d11082cea19f3df13a3562d" + +[[package]] +name = "rustls-webpki" +version = "0.102.5" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "f9a6fccd794a42c2c105b513a2f62bc3fd8f3ba57a4593677ceb0bd035164d78" +dependencies = [ + "ring", + "rustls-pki-types", + "untrusted", +] + [[package]] name = "rustversion" version = "1.0.17" @@ -2477,6 +2852,15 @@ dependencies = [ "bytemuck", ] +[[package]] +name = "same-file" +version = "1.0.6" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "93fc1dc3aaa9bfed95e02e6eadabb4baf7e3078b0bd1b4d7b6b0b68378900502" +dependencies = [ + "winapi-util", +] + [[package]] name = "scopeguard" version = "1.2.0" @@ -2568,6 +2952,19 @@ dependencies = [ "syn 2.0.66", ] +[[package]] +name = "serde_yaml" +version = "0.9.34+deprecated" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "6a8b1a1a2ebf674015cc02edccce75287f1a0130d394307b36743c2f5d504b47" +dependencies = [ + "indexmap", + "itoa", + "ryu", + "serde", + "unsafe-libyaml", +] + [[package]] name = "sha1" version = "0.10.6" @@ -2579,6 +2976,17 @@ dependencies = [ "digest", ] +[[package]] +name = "sha2" +version = "0.10.8" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "793db75ad2bcafc3ffa7c68b215fee268f537982cd901d132f89c6343f3a3dc8" +dependencies = [ + "cfg-if", + "cpufeatures", + "digest", +] + [[package]] name = "sharded-slab" version = "0.1.7" @@ -2647,6 +3055,12 @@ dependencies = [ "windows-sys 0.52.0", ] +[[package]] +name = "spin" +version = "0.9.8" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "6980e8d7511241f8acf4aebddbb1ff938df5eebe98691418c4468d0b72a96a67" + [[package]] name = "stable_deref_trait" version = "1.2.0" @@ -2713,6 +3127,12 @@ dependencies = [ "syn 2.0.66", ] +[[package]] +name = "subtle" +version = "2.6.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "13c2bddecc57b384dee18652358fb23172facb8a2c51ccc10d74c157bdea3292" + [[package]] name = "syn" version = "1.0.109" @@ -2735,6 +3155,12 @@ dependencies = [ "unicode-ident", ] +[[package]] +name = "sync_wrapper" +version = "1.0.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "a7065abeca94b6a8a577f9bd45aa0867a2238b74e8eb67cf10d492bc39351394" + [[package]] name = "synstructure" version = "0.13.1" @@ -2857,6 +3283,21 @@ dependencies = [ "zerovec", ] +[[package]] +name = "tinyvec" +version = "1.8.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "445e881f4f6d382d5f27c034e25eb92edd7c784ceab92a0937db7f2e9471b938" +dependencies = [ + "tinyvec_macros", +] + +[[package]] +name = "tinyvec_macros" +version = "0.1.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "1f3ccbac311fea05f86f61904b462b55fb3df8837a366dfc601a0161d0532f20" + [[package]] name = "tokio" version = "1.38.0" @@ -2874,6 +3315,17 @@ dependencies = [ "windows-sys 0.48.0", ] +[[package]] +name = "tokio-rustls" +version = "0.26.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "0c7bc40d0e5a97695bb96e27995cd3a08538541b0a846f65bba7a359f36700d4" +dependencies = [ + "rustls", + "rustls-pki-types", + "tokio", +] + [[package]] name = "tokio-util" version = "0.7.11" @@ -2904,6 +3356,33 @@ dependencies = [ "winnow", ] +[[package]] +name = "tower" +version = "0.4.13" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "b8fa9be0de6cf49e536ce1851f987bd21a43b771b09473c3549a6c853db37c1c" +dependencies = [ + "futures-core", + "futures-util", + "pin-project", + "pin-project-lite", + "tokio", + "tower-layer", + "tower-service", +] + +[[package]] +name = "tower-layer" +version = "0.3.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "c20c8dbed6283a09604c3e69b4b7eeb54e298b8a600d4d5ecb5ad39de609f1d0" + +[[package]] +name = "tower-service" +version = "0.3.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "b6bc1c9ce2b5135ac7f93c72918fc37feb872bdc6a5533a8b85eb4b86bfdae52" + [[package]] name = "tracing" version = "0.1.40" @@ -2993,6 +3472,12 @@ version = "0.4.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "22048bc95dfb2ffd05b1ff9a756290a009224b60b2f0e7525faeee7603851e63" +[[package]] +name = "try-lock" +version = "0.2.5" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "e421abadd41a4225275504ea4d6566923418b7f05506fbc9c0fe86ba7396114b" + [[package]] name = "typeid" version = "1.0.0" @@ -3005,6 +3490,15 @@ version = "1.17.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "42ff0bf0c66b8238c6f3b578df37d0b7848e55df8577b3f74f92a69acceeb825" +[[package]] +name = "unicase" +version = "2.7.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "f7d2d4dafb69621809a81864c9c1b864479e1235c0dd4e199924b9742439ed89" +dependencies = [ + "version_check", +] + [[package]] name = "unicode-ident" version = "1.0.12" @@ -3017,6 +3511,18 @@ version = "0.1.13" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "0336d538f7abc86d282a4189614dfaa90810dfc2c6f6427eaf88e16311dd225d" +[[package]] +name = "unsafe-libyaml" +version = "0.2.11" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "673aac59facbab8a9007c7f6108d11f63b603f7cabff99fabf650fea5c32b861" + +[[package]] +name = "untrusted" +version = "0.9.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "8ecb6da28b8a351d773b68d5825ac39017e680750f980f3a1a85cd8dd28a47c1" + [[package]] name = "url" version = "2.5.1" @@ -3046,6 +3552,50 @@ version = "0.2.2" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "06abde3611657adf66d383f00b093d7faecc7fa57071cce2578660c9f1010821" +[[package]] +name = "utoipa" +version = "4.2.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "c5afb1a60e207dca502682537fefcfd9921e71d0b83e9576060f09abc6efab23" +dependencies = [ + "indexmap", + "serde", + "serde_json", + "serde_yaml", + "utoipa-gen", +] + +[[package]] +name = "utoipa-gen" +version = "4.3.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "7bf0e16c02bc4bf5322ab65f10ab1149bdbcaa782cba66dc7057370a3f8190be" +dependencies = [ + "proc-macro-error", + "proc-macro2", + "quote", + "regex", + "syn 2.0.66", +] + +[[package]] +name = "utoipa-swagger-ui" +version = "7.1.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "943e0ff606c6d57d410fd5663a4d7c074ab2c5f14ab903b9514565e59fa1189e" +dependencies = [ + "actix-web", + "mime_guess", + "regex", + "reqwest", + "rust-embed", + "serde", + "serde_json", + "url", + "utoipa", + "zip", +] + [[package]] name = "valuable" version = "0.1.0" @@ -3073,6 +3623,25 @@ version = "0.9.4" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f" +[[package]] +name = "walkdir" +version = "2.5.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "29790946404f91d9c5d06f9874efddea1dc06c5efe94541a7d6863108e3a5e4b" +dependencies = [ + "same-file", + "winapi-util", +] + +[[package]] +name = "want" +version = "0.3.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "bfa7760aed19e106de2c7c0b581b509f2f25d3dacaf737cb82ac61bc6d760b0e" +dependencies = [ + "try-lock", +] + [[package]] name = "wasi" version = "0.11.0+wasi-snapshot-preview1" @@ -3104,6 +3673,18 @@ dependencies = [ "wasm-bindgen-shared", ] +[[package]] +name = "wasm-bindgen-futures" +version = "0.4.42" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "76bc14366121efc8dbb487ab05bcc9d346b3b5ec0eaa76e46594cabbe51762c0" +dependencies = [ + "cfg-if", + "js-sys", + "wasm-bindgen", + "web-sys", +] + [[package]] name = "wasm-bindgen-macro" version = "0.2.92" @@ -3133,6 +3714,25 @@ version = "0.2.92" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "af190c94f2773fdb3729c55b007a722abb5384da03bc0986df4c289bf5567e96" +[[package]] +name = "web-sys" +version = "0.3.69" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "77afa9a11836342370f4817622a2f0f418b134426d91a82dfb48f532d2ec13ef" +dependencies = [ + "js-sys", + "wasm-bindgen", +] + +[[package]] +name = "webpki-roots" +version = "0.26.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "bd7c23921eeb1713a4e851530e9b9756e4fb0e89978582942612524cf09f01cd" +dependencies = [ + "rustls-pki-types", +] + [[package]] name = "wide" version = "0.7.24" @@ -3159,6 +3759,15 @@ version = "0.4.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6" +[[package]] +name = "winapi-util" +version = "0.1.8" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "4d4cc384e1e73b93bafa6fb4f1df8c41695c8a91cf9c4c64358067d15a7b6c6b" +dependencies = [ + "windows-sys 0.52.0", +] + [[package]] name = "winapi-x86_64-pc-windows-gnu" version = "0.4.0" @@ -3322,6 +3931,16 @@ dependencies = [ "memchr", ] +[[package]] +name = "winreg" +version = "0.52.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "a277a57398d4bfa075df44f501a17cfdf8542d224f0d36095a2adc7aee4ef0a5" +dependencies = [ + "cfg-if", + "windows-sys 0.48.0", +] + [[package]] name = "write16" version = "1.0.0" @@ -3405,6 +4024,12 @@ dependencies = [ "synstructure", ] +[[package]] +name = "zeroize" +version = "1.8.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "ced3678a2879b30306d323f4542626697a464a97c0a07c9aebf7ebca65cd4dde" + [[package]] name = "zerovec" version = "0.10.2" @@ -3427,6 +4052,22 @@ dependencies = [ "syn 2.0.66", ] +[[package]] +name = "zip" +version = "1.1.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "9cc23c04387f4da0374be4533ad1208cbb091d5c11d070dfef13676ad6497164" +dependencies = [ + "arbitrary", + "crc32fast", + "crossbeam-utils", + "displaydoc", + "flate2", + "indexmap", + "num_enum", + "thiserror", +] + [[package]] name = "zstd" version = "0.13.1" diff --git a/Cargo.toml b/Cargo.toml index e3c9dac6..2420318a 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -27,8 +27,8 @@ biocommons-bioutils = "0.1.0" boolvec = "0.2" byteorder = "1.4" chrono = { version = "0.4", features = ["serde"] } -clap = { version = "4.5", features = ["derive", "env"] } clap-verbosity-flag = "2.2" +clap = { version = "4.5", features = ["derive", "env"] } csv = "1.2" enum-map = { version = "2.7.3", features = ["serde"] } env_logger = "0.11" @@ -42,16 +42,19 @@ pbjson = "0.7" pbjson-types = "0.7" prost = "0.13" rayon = "1.8" -rocksdb = { version = "0.22", features = ["multi-threaded-cf"] } rocksdb-utils-lookup = "0.4" +rocksdb = { version = "0.22", features = ["multi-threaded-cf"] } rustc-hash = "2.0.0" -serde = { version = "1.0", features = ["derive"] } serde_json = { version = "1.0", features = ["preserve_order"] } +serde = { version = "1.0", features = ["derive"] } serde_with = { version = "3.9", features = ["alloc", "macros", "indexmap_2"], default-features = false } +serde_yaml = "0.9" strum = { version = "0.26", features = ["strum_macros", "derive"] } thiserror = "1.0" 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"] } [dependencies.noodles] version = "0.77.0" diff --git a/build.rs b/build.rs index 20dc8a16..af2345bd 100644 --- a/build.rs +++ b/build.rs @@ -14,6 +14,7 @@ fn main() -> Result<(), anyhow::Error> { "annonars/clinvar/minimal.proto", "annonars/clinvar/per_gene.proto", "annonars/clinvar/sv.proto", + "annonars/common/versions.proto", "annonars/cons/base.proto", "annonars/dbsnp/base.proto", "annonars/functional/refseq.proto", @@ -50,6 +51,8 @@ fn main() -> Result<(), anyhow::Error> { // Override prost-types with pbjson-types .compile_well_known_types() .extern_path(".google.protobuf", "::pbjson_types") + // Derive the types for utoipa. + .message_attribute(".", "#[derive(utoipa::ToSchema)]") // Define the protobuf files to compile. .compile_protos(&proto_files, &[root])?; diff --git a/protos/annonars/common/versions.proto b/protos/annonars/common/versions.proto new file mode 100644 index 00000000..0060bcb3 --- /dev/null +++ b/protos/annonars/common/versions.proto @@ -0,0 +1,37 @@ +syntax = "proto3"; + +package annonars.common.versions; + +// Source that data was created from. +message CreatedFrom { + // The name of the data source. + string name = 1; + // The version of the data source. + string version = 2; +} + +// Version specification. +message VersionSpec { + // Identifier of the data. + string identifier = 1; + // Title of the data. + string title = 2; + // Creator of the data. + string creator = 3; + // Contributors of the data. + repeated string contributor = 4; + // Format of the data. + string format = 5; + // Date of the data. + string date = 6; + // Version of the data. + string version = 7; + // Optional genome release. + optional string genome_release = 8; + // Data description. + string description = 9; + // Data source. + repeated string source = 10; + // Created from information. + repeated CreatedFrom created_from = 11; +} diff --git a/src/common/cli.rs b/src/common/cli.rs index f67160fd..738b90fb 100644 --- a/src/common/cli.rs +++ b/src/common/cli.rs @@ -33,6 +33,8 @@ pub enum OutputFormat { strum::Display, strum::EnumString, enum_map::Enum, + serde::Serialize, + utoipa::ToSchema, )] #[strum(serialize_all = "lowercase")] pub enum GenomeRelease { diff --git a/src/main.rs b/src/main.rs index 4ced2134..5cbacb10 100644 --- a/src/main.rs +++ b/src/main.rs @@ -56,8 +56,8 @@ enum Commands { Regions(Regions), /// "db-utils" sub commands DbUtils(DbUtils), - /// "run-server" command. - RunServer(server::Args), + /// "server" sub command. + Server(Server), } /// Parsing of "gene" subcommand @@ -315,6 +315,23 @@ enum DbUtilsCommands { DumpMeta(db_utils::cli::dump_meta::Args), } +/// Parsing of "server" subcommands. +#[derive(Debug, Args, Clone)] +struct Server { + /// The sub command to run. + #[command(subcommand)] + command: ServerCommands, +} + +/// Enum supporting the parsing of "server *" subcommands. +#[derive(Debug, Subcommand, Clone)] +enum ServerCommands { + /// "run" sub command. + Run(server::run::Args), + /// Dump the schema. + Schema(crate::server::schema::Args), +} + pub fn main() -> Result<(), anyhow::Error> { let cli = Cli::parse(); @@ -417,7 +434,12 @@ pub fn main() -> Result<(), anyhow::Error> { db_utils::cli::dump_meta::run(&cli.common, args)? } }, - Commands::RunServer(args) => server::run(&cli.common, args)?, + Commands::Server(args) => match &args.command { + ServerCommands::Run(args) => server::run::run(&cli.common, args)?, + ServerCommands::Schema(args) => { + server::schema::run(&cli.common, args)?; + } + }, } Ok::<(), Error>(()) diff --git a/src/pbs/common.rs b/src/pbs/common.rs new file mode 100644 index 00000000..09ebb5fb --- /dev/null +++ b/src/pbs/common.rs @@ -0,0 +1,10 @@ +//! Code generate for protobufs by `prost-build`. + +/// Information about versions. +pub mod versions { + include!(concat!(env!("OUT_DIR"), "/annonars.common.versions.rs")); + include!(concat!( + env!("OUT_DIR"), + "/annonars.common.versions.serde.rs" + )); +} diff --git a/src/pbs/mod.rs b/src/pbs/mod.rs index 6d5177cd..2ff4b6e8 100644 --- a/src/pbs/mod.rs +++ b/src/pbs/mod.rs @@ -2,6 +2,7 @@ pub mod clinvar; pub mod clinvar_data; +pub mod common; pub mod cons; pub mod dbsnp; pub mod functional; diff --git a/src/regions/.editorconfig b/src/regions/.editorconfig new file mode 100644 index 00000000..c1322dc7 --- /dev/null +++ b/src/regions/.editorconfig @@ -0,0 +1,12 @@ +# EditorConfig is awesome: https://EditorConfig.org + +# top-most EditorConfig file +root = true + +[*] +indent_style = space +indent_size = 4 +end_of_line = lf +charset = utf-8 +trim_trailing_whitespace = false +insert_final_newline = false \ No newline at end of file diff --git a/src/server/actix_server/mod.rs b/src/server/actix_server/mod.rs deleted file mode 100644 index dbe816cd..00000000 --- a/src/server/actix_server/mod.rs +++ /dev/null @@ -1,41 +0,0 @@ -//! Implementation of the actix server. - -pub mod annos_db_info; -pub mod annos_range; -pub mod annos_variant; -pub mod clinvar_sv; -pub mod error; -pub mod fetch; -pub mod genes_clinvar; -pub mod genes_info; -pub mod genes_lookup; -pub mod genes_search; - -use actix_web::{middleware::Logger, web::Data, App, HttpServer}; - -use super::{Args, WebServerData}; - -/// Main entry point for the actix server. -/// -/// # Errors -/// -/// If the server cannot be started. -#[actix_web::main] -pub async fn main(args: &Args, dbs: Data) -> std::io::Result<()> { - HttpServer::new(move || { - let app = App::new() - .app_data(dbs.clone()) - .service(annos_variant::handle) - .service(annos_range::handle) - .service(annos_db_info::handle) - .service(clinvar_sv::handle) - .service(genes_clinvar::handle) - .service(genes_info::handle) - .service(genes_search::handle) - .service(genes_lookup::handle); - app.wrap(Logger::default()) - }) - .bind((args.listen_host.as_str(), args.listen_port))? - .run() - .await -} diff --git a/src/server/mod.rs b/src/server/mod.rs index 93bb0fd9..c58ed22e 100644 --- a/src/server/mod.rs +++ b/src/server/mod.rs @@ -1,503 +1,4 @@ //! Run REST API for serving entries from the annotations database -pub mod actix_server; - -use std::{collections::HashMap, time::Instant}; - -use clap::Parser; -use indicatif::ParallelProgressIterator; -use prost::Message; -use rayon::prelude::*; - -use crate::{ - clinvar_sv::cli::query::{self as clinvarsv_query, IntervalTrees as ClinvarsvIntervalTrees}, - common::{self, cli::GenomeRelease}, - pbs::genes, -}; - -/// Encode annotation database. -#[derive( - Debug, - Default, - Clone, - Copy, - PartialEq, - Eq, - PartialOrd, - Ord, - Hash, - strum::Display, - strum::EnumString, - strum::EnumIter, - serde::Serialize, - serde::Deserialize, - enum_map::Enum, -)] -#[strum(serialize_all = "snake_case")] -#[serde(rename_all = "snake_case")] -pub enum AnnoDb { - /// Other database. - #[default] - Other, - /// CADD annotations. - Cadd, - /// dbSNP annotations. - Dbsnp, - /// dbNSFP annotations. - Dbnsfp, - /// dbscSNV annotations. - Dbscsnv, - /// gnomAD mtDNA annotations. - GnomadMtdna, - /// gnomAD exomes annotations. - GnomadExomes, - /// gnomAD genomes annotations. - GnomadGenomes, - /// HelixMtDb annotations. - Helixmtdb, - /// UCSC conservation annotations. - UcscConservation, - /// ClinVar with minimal data extracted. - Clinvar, -} - -impl AnnoDb { - /// Return the expected column family name of the database. - pub fn cf_name(self) -> &'static str { - match self { - AnnoDb::Cadd => "tsv_data", - AnnoDb::Dbsnp => "dbsnp_data", - AnnoDb::Dbnsfp => "tsv_data", - AnnoDb::Dbscsnv => "tsv_data", - AnnoDb::GnomadMtdna => "gnomad_mtdna_data", - AnnoDb::GnomadExomes => "gnomad_nuclear_data", - AnnoDb::GnomadGenomes => "gnomad_nuclear_data", - AnnoDb::Helixmtdb => "helixmtdb_data", - AnnoDb::UcscConservation => "ucsc_conservation", - AnnoDb::Clinvar => "clinvar", - AnnoDb::Other => panic!("cannot get CF name for 'Other'"), - } - } - - /// Return the key for the database version. - fn db_version_meta(&self) -> Option<&'static str> { - match self { - AnnoDb::Cadd => Some("db-version"), - AnnoDb::Dbsnp => Some("db-version"), - AnnoDb::Dbnsfp => Some("db-version"), - AnnoDb::Dbscsnv => Some("db-version"), - AnnoDb::GnomadMtdna => Some("gnomad-version"), - AnnoDb::GnomadExomes => Some("gnomad-version"), - AnnoDb::GnomadGenomes => Some("gnomad-version"), - AnnoDb::Helixmtdb => None, - AnnoDb::UcscConservation => None, - AnnoDb::Clinvar => None, - AnnoDb::Other => panic!("cannot get meta version name name for 'Other'"), - } - } -} - -/// Identifier / name information for one gene. -#[derive(Debug, serde::Serialize, serde::Deserialize, Clone)] -pub struct GeneNames { - /// HGNC gene ID. - pub hgnc_id: String, - /// HGNC gene symbol. - pub symbol: String, - /// Gene name from HGNC. - pub name: String, - /// HGNC alias symbols. - pub alias_symbol: Vec, - /// HGNC alias names. - pub alias_name: Vec, - /// ENSEMBL gene ID. - pub ensembl_gene_id: Option, - /// NCBI gene ID. - pub ncbi_gene_id: Option, -} - -/// Gene information database. -#[derive(Debug)] -pub struct GeneInfoDb { - /// The database with overall genes information. - pub db: rocksdb::DBWithThreadMode, - /// ClinVar gene information. - pub db_clinvar: Option>, - /// Gene information to keep in memory (for `/genes/search`). - pub gene_names: Vec, - /// Mapping from allowed gene name string to index in `gene_names`. - pub name_to_hgnc_idx: HashMap, -} - -/// Genome-release specific annotation for each database. -pub type ReleaseAnnos = - enum_map::EnumMap>>; - -/// Database information -#[derive(serde::Serialize, Debug, Clone, Default)] -pub struct DbInfo { - /// Identifier of the database. - pub name: AnnoDb, - /// Version of the database. - pub db_version: Option, - /// Version of the builder code. - pub builder_version: String, -} - -/// Fetch database information from the given RocksDB. -fn fetch_db_info( - db: &rocksdb::DBWithThreadMode, - name: AnnoDb, -) -> Result<(GenomeRelease, DbInfo), anyhow::Error> { - let genome_release: GenomeRelease = rocksdb_utils_lookup::fetch_meta(db, "genome-release")? - .ok_or(anyhow::anyhow!("meta:genome-release not found in data"))? - .as_str() - .parse()?; - let db_version = name - .db_version_meta() - .map(|db_version_meta| { - rocksdb_utils_lookup::fetch_meta(db, db_version_meta)?.ok_or(anyhow::anyhow!( - "meta:{} not found in database", - db_version_meta - )) - }) - .transpose()?; - let builder_version = - rocksdb_utils_lookup::fetch_meta(db, "annonars-version")?.ok_or(anyhow::anyhow!( - "meta:annonars-version not found in database {}", - db.path().display() - ))?; - let db_info = DbInfo { - name, - db_version, - builder_version, - }; - Ok((genome_release, db_info)) -} - -/// Data for the web server. -#[derive(Debug, Default)] -pub struct WebServerData { - /// Gene information database. - pub genes: Option, - /// Release-specific annotations for each `GenomeRelease`. - pub annos: enum_map::EnumMap, - /// Release-specific ClinVar SV interval tree indexed databased. - pub clinvar_svs: enum_map::EnumMap>, - /// Version information for each database. - pub db_infos: enum_map::EnumMap>>, -} - -/// Command line arguments for `server rest` sub command. -/// -/// Each path can be given more than one time to support multiple releases. When the server -/// is started, it needs to be given a file for each database with each release. -#[derive(Parser, Debug, Clone)] -#[command(author, version, about = "Run annonars REST API", long_about = None)] -pub struct Args { - /// Path to genes database. - #[arg(long)] - pub path_genes: Option, - /// ClinVar per-gene database(s), one for each release. - #[arg(long)] - pub path_clinvar_genes: Option, - /// ClinVar database(s), one for each release. - #[arg(long)] - pub path_clinvar: Vec, - /// ClinVar SV database(s), one for each release. - #[arg(long)] - pub path_clinvar_sv: Vec, - /// CADD database(s), one for each release. - #[arg(long)] - pub path_cadd: Vec, - /// dbSNP database(s), one for each release. - #[arg(long)] - pub path_dbsnp: Vec, - /// dbNSFP database(s), one for each release. - #[arg(long)] - pub path_dbnsfp: Vec, - /// PdbscSNV database(s), one for each release. - #[arg(long)] - pub path_dbscsnv: Vec, - /// gnomAD mtDNA database(s), one for each release. - #[arg(long)] - pub path_gnomad_mtdna: Vec, - /// gnomAD-exomes database(s), one for each release. - #[arg(long)] - pub path_gnomad_exomes: Vec, - /// gnomAD-genomes database(s), one for each release. - #[arg(long)] - pub path_gnomad_genomes: Vec, - /// HelixMtDB database(s), one for each release. - #[arg(long)] - pub path_helixmtdb: Vec, - /// UCSC conservation database(s), one for each release. - #[arg(long)] - pub path_ucsc_conservation: Vec, - - /// IP to listen on. - #[arg(long, default_value = "127.0.0.1")] - pub listen_host: String, - /// Port to listen on. - #[arg(long, default_value_t = 8081)] - pub listen_port: u16, -} - -/// Open a RocksDB database. -/// -/// # Arguments -/// -/// * `path` - Path to the database. -/// * `cf_name` - Name of the column family to open (besides the mandatory `meta` column family). -fn open_db( - path: &str, - cf_name: &str, -) -> Result, anyhow::Error> { - tracing::info!("Opening database {}...", path); - let before_open = Instant::now(); - let res = rocksdb::DB::open_cf_for_read_only( - &rocksdb::Options::default(), - common::readlink_f(path)?, - ["meta", cf_name], - true, - ) - .map_err(|e| anyhow::anyhow!("problem opening database: {}", e)); - tracing::info!("...done opening database in {:?}", before_open.elapsed()); - res -} - -/// Obtain gene names from the genes RocksDB. -fn extract_gene_names( - genes_db: &rocksdb::DBWithThreadMode, -) -> Result, anyhow::Error> { - let mut result = Vec::new(); - - let cf_read = genes_db.cf_handle("genes").unwrap(); - let mut iter = genes_db.raw_iterator_cf(&cf_read); - iter.seek(b""); - while iter.valid() { - if let Some(iter_value) = iter.value() { - let record = genes::base::Record::decode(std::io::Cursor::new(iter_value))?; - let genes::base::Record { hgnc, .. } = record; - if let Some(hgnc) = hgnc { - let genes::base::HgncRecord { - hgnc_id, - symbol, - name, - alias_symbol, - alias_name, - ensembl_gene_id, - entrez_id, - .. - } = hgnc; - result.push(GeneNames { - hgnc_id, - symbol, - name, - alias_symbol, - alias_name, - ensembl_gene_id, - ncbi_gene_id: entrez_id, - }) - } - } - iter.next(); - } - - Ok(result) -} - -/// Main entry point for `server rest` sub command. -pub fn run(args_common: &common::cli::Args, args: &Args) -> Result<(), anyhow::Error> { - 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")); - } - _ => (), - } - } - - tracing::info!("Opening databases..."); - let mut data = WebServerData::default(); - let before_opening = Instant::now(); - - if let Some(path_genes) = args.path_genes.as_ref() { - tracing::info!("Opening genes database {}...", path_genes); - let before_open = Instant::now(); - let db = open_db(path_genes, "genes")?; - tracing::info!( - "...done opening genes database in {:?}", - before_open.elapsed() - ); - - let db_clinvar = if let Some(path_clinvar_genes) = args.path_clinvar_genes.as_ref() { - tracing::info!("Opening ClinVar genes database {}...", path_clinvar_genes); - let before_open = Instant::now(); - let clinvar_db = open_db(path_clinvar_genes, "clinvar-genes")?; - tracing::info!( - "...done opening ClinVar genes database in {:?}", - before_open.elapsed() - ); - Some(clinvar_db) - } else { - None - }; - - tracing::info!("Building gene names..."); - let before_open = Instant::now(); - let gene_names = extract_gene_names(&db)?; - let name_to_hgnc_idx = { - let mut result = HashMap::new(); - for (idx, gene_name) in gene_names.iter().enumerate() { - result.insert(gene_name.hgnc_id.clone(), idx); - if let Some(ensembl_gene_id) = gene_name.ensembl_gene_id.as_ref() { - result.insert(ensembl_gene_id.clone(), idx); - } - if let Some(ncbi_gene_id) = gene_name.ncbi_gene_id.as_ref() { - result.insert(ncbi_gene_id.clone(), idx); - } - result.insert(gene_name.symbol.clone(), idx); - } - result - }; - tracing::info!("...done building genes names {:?}", before_open.elapsed()); - data.genes = Some(GeneInfoDb { - db, - db_clinvar, - gene_names, - name_to_hgnc_idx, - }); - } - - tracing::info!("Opening ClinVar SV databases..."); - let before_clinvar_sv = Instant::now(); - for path_clinvar_sv in &args.path_clinvar_sv { - tracing::info!(" - {}", path_clinvar_sv); - let (clinvar_sv_db, clinvar_sv_meta) = clinvarsv_query::open_rocksdb( - path_clinvar_sv, - "clinvar_sv", - "meta", - "clinvar_sv_by_rcv", - ) - .map_err(|e| anyhow::anyhow!("problem opening RocksDB database: {}", e))?; - let genome_release: GenomeRelease = clinvar_sv_meta.genome_release.parse()?; - tracing::info!(" => {}", genome_release); - let clinvar_sv_interval_trees = - ClinvarsvIntervalTrees::with_db(clinvar_sv_db, "clinvar_sv", clinvar_sv_meta) - .map_err(|e| anyhow::anyhow!("problem building interval trees: {}", e))?; - data.clinvar_svs[genome_release] = Some(clinvar_sv_interval_trees); - } - tracing::info!( - "...done opening ClinVar SV databases in {:?}", - before_clinvar_sv.elapsed() - ); - - // Argument lists from the command line with the corresponding database enum value. - let paths_db_pairs = [ - (&args.path_clinvar, AnnoDb::Clinvar), - (&args.path_cadd, AnnoDb::Cadd), - (&args.path_dbnsfp, AnnoDb::Dbnsfp), - (&args.path_dbsnp, AnnoDb::Dbsnp), - (&args.path_dbscsnv, AnnoDb::Dbscsnv), - (&args.path_gnomad_mtdna, AnnoDb::GnomadMtdna), - (&args.path_gnomad_exomes, AnnoDb::GnomadExomes), - (&args.path_gnomad_genomes, AnnoDb::GnomadGenomes), - (&args.path_helixmtdb, AnnoDb::Helixmtdb), - (&args.path_ucsc_conservation, AnnoDb::UcscConservation), - ]; - // "Unpack" the list of paths to single paths. - let path_db_pairs = paths_db_pairs - .iter() - .map(|(paths, anno_db)| { - paths - .iter() - .map(|path| (path.clone(), *anno_db)) - .collect::>() - }) - .collect::>() - .into_iter() - .flatten() - .collect::>(); - // Open the corresponding databases in parallel and extract database infos. Store the - // resulting database infos in `data`. - path_db_pairs - .par_iter() - .progress_with(crate::common::cli::progress_bar(path_db_pairs.len())) - .map(|(path, anno_db)| -> Result<_, anyhow::Error> { - let db = open_db(path, anno_db.cf_name())?; - let (genome_release, db_info) = fetch_db_info(&db, *anno_db)?; - - Ok((db_info, genome_release, db)) - }) - .collect::, _>>()? - .into_iter() - .for_each(|(db_info, genome_release, db)| { - let name = db_info.name; - data.db_infos[genome_release][name] = Some(db_info); - data.annos[genome_release][name] = Some(db); - }); - tracing::info!( - "...done opening databases in {:?}", - before_opening.elapsed() - ); - - tracing::info!( - "Launching server main on http://{}:{} ...", - args.listen_host.as_str(), - args.listen_port - ); - tracing::info!( - " try: http://{}:{}/genes/search?q=BRCA", - args.listen_host.as_str(), - args.listen_port - ); - tracing::info!( - " try: http://{}:{}/genes/search?q=BRCA&fields=hgnc_id,ensembl_gene_id,ncbi_gene_id,symbol", - args.listen_host.as_str(), - args.listen_port - ); - tracing::info!( - " try: http://{}:{}/genes/lookup?q=BRCA,BRCA1,HGNC:1100", - args.listen_host.as_str(), - args.listen_port - ); - tracing::info!( - " try: http://{}:{}/genes/info?hgnc_id=HGNC:12403", - args.listen_host.as_str(), - args.listen_port - ); - tracing::info!( - " try: http://{}:{}/genes/clinvar?hgnc_id=HGNC:12403", - args.listen_host.as_str(), - args.listen_port - ); - tracing::info!( - " try: http://{}:{}/annos/db-info?genome_release=grch37", - args.listen_host.as_str(), - args.listen_port - ); - tracing::info!( - " try: http://{}:{}/annos/variant?genome_release=grch37&chromosome=1&pos=55505599&reference=C&alternative=G", - args.listen_host.as_str(), - args.listen_port - ); - tracing::info!( - " try: http://{}:{}/annos/variant?genome_release=grch37&chromosome=1&pos=10001&reference=T&alternative=A", - args.listen_host.as_str(), - args.listen_port - ); - tracing::info!( - " try: http://{}:{}/annos/range?genome_release=grch37&chromosome=1&start=1&stop=55516888", - args.listen_host.as_str(), - args.listen_port - ); - actix_server::main(args, actix_web::web::Data::new(data))?; - - tracing::info!("All done. Have a nice day!"); - Ok(()) -} +pub mod run; +pub mod schema; diff --git a/src/server/actix_server/annos_db_info.rs b/src/server/run/annos_db_info.rs similarity index 100% rename from src/server/actix_server/annos_db_info.rs rename to src/server/run/annos_db_info.rs diff --git a/src/server/actix_server/annos_range.rs b/src/server/run/annos_range.rs similarity index 94% rename from src/server/actix_server/annos_range.rs rename to src/server/run/annos_range.rs index 9d2708f6..37903e50 100644 --- a/src/server/actix_server/annos_range.rs +++ b/src/server/run/annos_range.rs @@ -10,8 +10,8 @@ use strum::IntoEnumIterator; use crate::{ common::{keys, version}, server::{ - actix_server::fetch::{fetch_pos_protobuf, fetch_pos_tsv_json}, - AnnoDb, + run::fetch::{fetch_pos_protobuf, fetch_pos_tsv_json}, + run::AnnoDb, }, }; @@ -98,7 +98,7 @@ async fn handle( .as_ref() .map(|db| { fetch_pos_protobuf::( - db, + &db.data, anno_db.cf_name(), query.start_pos(), query.stop_pos(), @@ -112,7 +112,7 @@ async fn handle( .as_ref() .map(|db| { fetch_pos_tsv_json( - db, + &db.data, anno_db.cf_name(), query.start_pos(), query.stop_pos(), @@ -126,7 +126,7 @@ async fn handle( .as_ref() .map(|db| { fetch_pos_protobuf::( - db, + &db.data, anno_db.cf_name(), query.start_pos(), query.stop_pos(), @@ -140,7 +140,7 @@ async fn handle( .as_ref() .map(|db| { fetch_pos_protobuf::( - db, + &db.data, anno_db.cf_name(), query.start_pos(), query.stop_pos(), @@ -154,7 +154,7 @@ async fn handle( .as_ref() .map(|db| { fetch_pos_protobuf::( - db, + &db.data, anno_db.cf_name(), query.start_pos(), query.stop_pos(), @@ -176,14 +176,14 @@ async fn handle( if db_version.starts_with("2.") { fetch_pos_protobuf::( - db, + &db.data, anno_db.cf_name(), query.start_pos(), query.stop_pos(), ) } else if db_version.starts_with("4.") { fetch_pos_protobuf::( - db, + &db.data, anno_db.cf_name(), query.start_pos(), query.stop_pos(), @@ -210,21 +210,21 @@ async fn handle( .expect("gnomAD must have db version"); if db_version.starts_with("2.") { fetch_pos_protobuf::( - db, + &db.data, anno_db.cf_name(), query.start_pos(), query.stop_pos(), ) } else if db_version.starts_with("3.") { fetch_pos_protobuf::( - db, + &db.data, anno_db.cf_name(), query.start_pos(), query.stop_pos(), ) } else if db_version.starts_with("4.") { fetch_pos_protobuf::( - db, + &db.data, anno_db.cf_name(), query.start_pos(), query.stop_pos(), @@ -244,7 +244,7 @@ async fn handle( .as_ref() .map(|db| { fetch_pos_protobuf::( - db, + &db.data, anno_db.cf_name(), query.start_pos(), query.stop_pos(), diff --git a/src/server/actix_server/annos_variant.rs b/src/server/run/annos_variant.rs similarity index 92% rename from src/server/actix_server/annos_variant.rs rename to src/server/run/annos_variant.rs index 0a5ec6c8..1ddd66d7 100644 --- a/src/server/actix_server/annos_variant.rs +++ b/src/server/run/annos_variant.rs @@ -8,7 +8,7 @@ use strum::IntoEnumIterator; use crate::{ common::{keys, version}, - server::AnnoDb, + server::run::AnnoDb, }; use super::error::CustomError; @@ -70,7 +70,7 @@ struct Container { #[allow(clippy::option_map_unit_fn)] #[get("/annos/variant")] async fn handle( - data: Data, + data: Data, _path: Path<()>, query: web::Query, ) -> actix_web::Result { @@ -93,7 +93,7 @@ async fn handle( .as_ref() .map(|db| { fetch_var_protobuf::( - db, + &db.data, anno_db.cf_name(), query.clone().into_inner().into(), ) @@ -105,7 +105,11 @@ async fn handle( data.annos[genome_release][anno_db] .as_ref() .map(|db| { - fetch_var_tsv_json(db, anno_db.cf_name(), query.clone().into_inner().into()) + fetch_var_tsv_json( + &db.data, + anno_db.cf_name(), + query.clone().into_inner().into(), + ) }) .transpose()? .map(|v| annotations.insert(anno_db, v)); @@ -115,7 +119,7 @@ async fn handle( .as_ref() .map(|db| { fetch_var_protobuf::( - db, + &db.data, anno_db.cf_name(), query.clone().into_inner().into(), ) @@ -128,7 +132,7 @@ async fn handle( .as_ref() .map(|db| { fetch_var_protobuf::( - db, + &db.data, anno_db.cf_name(), query.clone().into_inner().into(), ) @@ -141,7 +145,7 @@ async fn handle( .as_ref() .map(|db| { fetch_var_protobuf::( - db, + &db.data, anno_db.cf_name(), query.clone().into_inner().into(), ) @@ -162,13 +166,13 @@ async fn handle( if db_version.starts_with("2.") { fetch_var_protobuf::( - db, + &db.data, anno_db.cf_name(), query.clone().into_inner().into(), ) } else if db_version.starts_with("4.") { fetch_var_protobuf::( - db, + &db.data, anno_db.cf_name(), query.clone().into_inner().into(), ) @@ -194,19 +198,19 @@ async fn handle( .expect("gnomAD must have db version"); if db_version.starts_with("2.") { fetch_var_protobuf::( - db, + &db.data, anno_db.cf_name(), query.clone().into_inner().into(), ) } else if db_version.starts_with("3.") { fetch_var_protobuf::( - db, + &db.data, anno_db.cf_name(), query.clone().into_inner().into(), ) } else if db_version.starts_with("4.") { fetch_var_protobuf::( - db, + &db.data, anno_db.cf_name(), query.clone().into_inner().into(), ) @@ -231,7 +235,7 @@ async fn handle( }; let stop = query.clone().into_inner().into(); fetch_pos_protobuf::( - db, + &db.data, anno_db.cf_name(), start, stop, diff --git a/src/server/actix_server/clinvar_sv.rs b/src/server/run/clinvar_sv.rs similarity index 99% rename from src/server/actix_server/clinvar_sv.rs rename to src/server/run/clinvar_sv.rs index 26fa45d3..11d46b91 100644 --- a/src/server/actix_server/clinvar_sv.rs +++ b/src/server/run/clinvar_sv.rs @@ -73,7 +73,7 @@ where #[allow(clippy::option_map_unit_fn)] #[get("/clinvar-sv/query")] async fn handle( - data: Data, + data: Data, _path: Path<()>, query: web::Query, ) -> actix_web::Result { diff --git a/src/server/actix_server/error.rs b/src/server/run/error.rs similarity index 100% rename from src/server/actix_server/error.rs rename to src/server/run/error.rs diff --git a/src/server/actix_server/fetch.rs b/src/server/run/fetch.rs similarity index 100% rename from src/server/actix_server/fetch.rs rename to src/server/run/fetch.rs diff --git a/src/server/actix_server/genes_clinvar.rs b/src/server/run/genes_clinvar.rs similarity index 97% rename from src/server/actix_server/genes_clinvar.rs rename to src/server/run/genes_clinvar.rs index 495fd834..67e02024 100644 --- a/src/server/actix_server/genes_clinvar.rs +++ b/src/server/run/genes_clinvar.rs @@ -36,7 +36,7 @@ struct Container { #[allow(clippy::option_map_unit_fn)] #[get("/genes/clinvar")] async fn handle( - data: Data, + data: Data, _path: Path<()>, query: web::Query, ) -> actix_web::Result { @@ -44,6 +44,7 @@ async fn handle( "genes database not available" )))?; let db_clinvar = genes_db + .data .db_clinvar .as_ref() .ok_or(CustomError::new(anyhow::anyhow!( diff --git a/src/server/actix_server/genes_info.rs b/src/server/run/genes_info.rs similarity index 93% rename from src/server/actix_server/genes_info.rs rename to src/server/run/genes_info.rs index 61a7f956..ec6028b4 100644 --- a/src/server/actix_server/genes_info.rs +++ b/src/server/run/genes_info.rs @@ -36,7 +36,7 @@ struct Container { #[allow(clippy::option_map_unit_fn)] #[get("/genes/info")] async fn handle( - data: Data, + data: Data, _path: Path<()>, query: web::Query, ) -> actix_web::Result { @@ -44,13 +44,14 @@ async fn handle( "genes database not available" )))?; let cf_genes = genes_db + .data .db .cf_handle("genes") .expect("no 'genes' column family"); let mut genes = indexmap::IndexMap::new(); if let Some(hgnc_id) = query.hgnc_id.as_ref() { for hgnc_id in hgnc_id { - if let Some(raw_buf) = genes_db.db.get_cf(&cf_genes, hgnc_id).map_err(|e| { + if let Some(raw_buf) = genes_db.data.db.get_cf(&cf_genes, hgnc_id).map_err(|e| { CustomError::new(anyhow::anyhow!("problem querying database: {}", e)) })? { let record = @@ -65,10 +66,12 @@ async fn handle( } let cf_meta = genes_db + .data .db .cf_handle("meta") .expect("no 'meta' column family"); let raw_builder_version = &genes_db + .data .db .get_cf(&cf_meta, "builder-version") .map_err(|e| CustomError::new(anyhow::anyhow!("problem querying database: {}", e)))? diff --git a/src/server/actix_server/genes_lookup.rs b/src/server/run/genes_lookup.rs similarity index 90% rename from src/server/actix_server/genes_lookup.rs rename to src/server/run/genes_lookup.rs index 37385bc2..a14e96b3 100644 --- a/src/server/actix_server/genes_lookup.rs +++ b/src/server/run/genes_lookup.rs @@ -8,7 +8,7 @@ use actix_web::{ Responder, }; -use crate::server::GeneNames; +use crate::server::run::GeneNames; use super::error::CustomError; use serde_with::{formats::CommaSeparator, StringWithSeparator}; @@ -37,7 +37,7 @@ struct Container { #[allow(clippy::option_map_unit_fn)] #[get("/genes/lookup")] async fn handle( - data: Data, + data: Data, _path: Path<()>, query: web::Query, ) -> actix_web::Result { @@ -47,9 +47,10 @@ async fn handle( let genes = indexmap::IndexMap::from_iter(query.q.iter().map(|q| { let v = genes_db + .data .name_to_hgnc_idx .get(q) - .map(|idx| genes_db.gene_names[*idx].clone()); + .map(|idx| genes_db.data.gene_names[*idx].clone()); (q.clone(), v) })); diff --git a/src/server/actix_server/genes_search.rs b/src/server/run/genes_search.rs similarity index 98% rename from src/server/actix_server/genes_search.rs rename to src/server/run/genes_search.rs index bfb5f13c..6e0ab3f5 100644 --- a/src/server/actix_server/genes_search.rs +++ b/src/server/run/genes_search.rs @@ -8,7 +8,7 @@ use actix_web::{ Responder, }; -use crate::server::GeneNames; +use crate::server::run::GeneNames; use super::error::CustomError; use serde_with::{formats::CommaSeparator, StringWithSeparator}; @@ -81,7 +81,7 @@ struct Container { #[allow(clippy::option_map_unit_fn)] #[get("/genes/search")] async fn handle( - data: Data, + data: Data, _path: Path<()>, query: web::Query, ) -> actix_web::Result { @@ -130,6 +130,7 @@ async fn handle( let fields_contains = |field: &Fields| -> bool { fields.is_empty() || fields.contains(field) }; let mut genes = genes_db + .data .gene_names .iter() .map(|gn| -> Scored { diff --git a/src/server/run/mod.rs b/src/server/run/mod.rs new file mode 100644 index 00000000..fb197e99 --- /dev/null +++ b/src/server/run/mod.rs @@ -0,0 +1,641 @@ +//! Implementation of the actix server. + +pub mod annos_db_info; +pub mod annos_range; +pub mod annos_variant; +pub mod clinvar_sv; +pub mod error; +pub mod fetch; +pub mod genes_clinvar; +pub mod genes_info; +pub mod genes_lookup; +pub mod genes_search; +pub mod versions; + +use std::{ + collections::HashMap, + path::{Path, PathBuf}, + str::FromStr as _, + time::Instant, +}; + +use clap::Parser; +use indicatif::ParallelProgressIterator; +use prost::Message; +use rayon::prelude::*; +use utoipa::OpenApi as _; + +use crate::{ + clinvar_sv::cli::query::{self as clinvarsv_query, IntervalTrees as ClinvarsvIntervalTrees}, + common::{self, cli::GenomeRelease}, + pbs::{self, genes}, +}; + +use actix_web::{middleware::Logger, web::Data, App, HttpServer}; + +/// Module with OpenAPI documentation. +pub mod openapi { + use crate::{ + common::cli::GenomeRelease, + pbs::common::versions::{CreatedFrom, VersionSpec}, + server::run::{ + versions::{AnnoVersionInfo, ReleaseVersionInfos}, + AnnoDb, + }, + }; + + use super::versions::{self, VersionInfoResponse}; + + /// Utoipa-based `OpenAPI` generation helper. + #[derive(utoipa::OpenApi)] + #[openapi( + paths(versions::handle), + components(schemas( + AnnoVersionInfo, + ReleaseVersionInfos, + VersionInfoResponse, + CreatedFrom, + VersionSpec, + GenomeRelease, + AnnoDb, + )) + )] + pub struct ApiDoc; +} + +/// Main entry point for the actix server. +/// +/// # Errors +/// +/// If the server cannot be started. +#[actix_web::main] +pub async fn main(args: &Args, dbs: Data) -> std::io::Result<()> { + let openapi = openapi::ApiDoc::openapi(); + + HttpServer::new(move || { + let app = App::new() + .app_data(dbs.clone()) + .service(annos_variant::handle) + .service(annos_range::handle) + .service(annos_db_info::handle) + .service(clinvar_sv::handle) + .service(genes_clinvar::handle) + .service(genes_info::handle) + .service(genes_search::handle) + .service(genes_lookup::handle) + .service(versions::handle) + .service( + utoipa_swagger_ui::SwaggerUi::new("/swagger-ui/{_:.*}") + .url("/api-docs/openapi.json", openapi.clone()), + ); + app.wrap(Logger::default()) + }) + .bind((args.listen_host.as_str(), args.listen_port))? + .run() + .await +} + +/// Encode annotation database. +#[derive( + Debug, + Default, + Clone, + Copy, + PartialEq, + Eq, + PartialOrd, + Ord, + Hash, + strum::Display, + strum::EnumString, + strum::EnumIter, + serde::Serialize, + serde::Deserialize, + enum_map::Enum, + utoipa::ToSchema, +)] +#[strum(serialize_all = "snake_case")] +#[serde(rename_all = "snake_case")] +pub enum AnnoDb { + /// Other database. + #[default] + Other, + /// CADD annotations. + Cadd, + /// dbSNP annotations. + Dbsnp, + /// dbNSFP annotations. + Dbnsfp, + /// dbscSNV annotations. + Dbscsnv, + /// gnomAD mtDNA annotations. + GnomadMtdna, + /// gnomAD exomes annotations. + GnomadExomes, + /// gnomAD genomes annotations. + GnomadGenomes, + /// HelixMtDb annotations. + Helixmtdb, + /// UCSC conservation annotations. + UcscConservation, + /// ClinVar with minimal data extracted. + Clinvar, +} + +impl AnnoDb { + /// Return the expected column family name of the database. + pub fn cf_name(self) -> &'static str { + match self { + AnnoDb::Cadd => "tsv_data", + AnnoDb::Dbsnp => "dbsnp_data", + AnnoDb::Dbnsfp => "tsv_data", + AnnoDb::Dbscsnv => "tsv_data", + AnnoDb::GnomadMtdna => "gnomad_mtdna_data", + AnnoDb::GnomadExomes => "gnomad_nuclear_data", + AnnoDb::GnomadGenomes => "gnomad_nuclear_data", + AnnoDb::Helixmtdb => "helixmtdb_data", + AnnoDb::UcscConservation => "ucsc_conservation", + AnnoDb::Clinvar => "clinvar", + AnnoDb::Other => panic!("cannot get CF name for 'Other'"), + } + } + + /// Return the key for the database version. + fn db_version_meta(&self) -> Option<&'static str> { + match self { + AnnoDb::Cadd => Some("db-version"), + AnnoDb::Dbsnp => Some("db-version"), + AnnoDb::Dbnsfp => Some("db-version"), + AnnoDb::Dbscsnv => Some("db-version"), + AnnoDb::GnomadMtdna => Some("gnomad-version"), + AnnoDb::GnomadExomes => Some("gnomad-version"), + AnnoDb::GnomadGenomes => Some("gnomad-version"), + AnnoDb::Helixmtdb => None, + AnnoDb::UcscConservation => None, + AnnoDb::Clinvar => None, + AnnoDb::Other => panic!("cannot get meta version name name for 'Other'"), + } + } +} + +/// Identifier / name information for one gene. +#[derive(Debug, serde::Serialize, serde::Deserialize, Clone)] +pub struct GeneNames { + /// HGNC gene ID. + pub hgnc_id: String, + /// HGNC gene symbol. + pub symbol: String, + /// Gene name from HGNC. + pub name: String, + /// HGNC alias symbols. + pub alias_symbol: Vec, + /// HGNC alias names. + pub alias_name: Vec, + /// ENSEMBL gene ID. + pub ensembl_gene_id: Option, + /// NCBI gene ID. + pub ncbi_gene_id: Option, +} + +/// Gene information database. +#[derive(Debug)] +pub struct GeneInfoDb { + /// The database with overall genes information. + pub db: rocksdb::DBWithThreadMode, + /// ClinVar gene information. + pub db_clinvar: Option>, + /// Gene information to keep in memory (for `/genes/search`). + pub gene_names: Vec, + /// Mapping from allowed gene name string to index in `gene_names`. + pub name_to_hgnc_idx: HashMap, +} + +/// Genome-release specific annotation for each database. +pub type ReleaseAnnos = enum_map::EnumMap< + AnnoDb, + Option>>, +>; + +/// Database information +#[derive(serde::Serialize, Debug, Clone, Default)] +pub struct DbInfo { + /// Identifier of the database. + pub name: AnnoDb, + /// Version of the database. + pub db_version: Option, + /// Version of the builder code. + pub builder_version: String, +} + +/// Fetch database information from the given RocksDB. +fn fetch_db_info( + db: &rocksdb::DBWithThreadMode, + name: AnnoDb, +) -> Result<(GenomeRelease, DbInfo), anyhow::Error> { + let genome_release: GenomeRelease = rocksdb_utils_lookup::fetch_meta(db, "genome-release")? + .ok_or(anyhow::anyhow!("meta:genome-release not found in data"))? + .as_str() + .parse()?; + let db_version = name + .db_version_meta() + .map(|db_version_meta| { + rocksdb_utils_lookup::fetch_meta(db, db_version_meta)?.ok_or(anyhow::anyhow!( + "meta:{} not found in database", + db_version_meta + )) + }) + .transpose()?; + let builder_version = + rocksdb_utils_lookup::fetch_meta(db, "annonars-version")?.ok_or(anyhow::anyhow!( + "meta:annonars-version not found in database {}", + db.path().display() + ))?; + let db_info = DbInfo { + name, + db_version, + builder_version, + }; + Ok((genome_release, db_info)) +} + +/// Generic type to store a database together with version specification. +#[derive(Debug)] +pub struct WithVersionSpec { + /// The actual data. + pub data: T, + /// Version specification. + pub version_spec: pbs::common::versions::VersionSpec, +} + +impl WithVersionSpec +where + T: std::fmt::Debug, +{ + /// Construct with the given data and path to specification YAML file. + pub fn from_data_and_path

(data: T, path: P) -> Result + where + P: AsRef, + { + let version_spec: pbs::common::versions::VersionSpec = + versions::schema::VersionSpec::from_path(path)?.into(); + Ok(Self { data, version_spec }) + } +} + +/// Data for the web server. +#[derive(Debug, Default)] +pub struct WebServerData { + /// Gene information database. + pub genes: Option>, + /// Release-specific annotations for each `GenomeRelease`. + pub annos: enum_map::EnumMap, + /// Release-specific ClinVar SV interval tree indexed databased. + pub clinvar_svs: enum_map::EnumMap>, + /// Version information for each database. + pub db_infos: enum_map::EnumMap>>, +} + +/// Command line arguments for `server rest` sub command. +/// +/// Each path can be given more than one time to support multiple releases. When the server +/// is started, it needs to be given a file for each database with each release. +#[derive(Parser, Debug, Clone)] +#[command(author, version, about = "Run annonars REST API", long_about = None)] +pub struct Args { + /// Path to genes database. + #[arg(long)] + pub path_genes: Option, + /// ClinVar per-gene database(s), one for each release. + #[arg(long)] + pub path_clinvar_genes: Option, + /// ClinVar database(s), one for each release. + #[arg(long)] + pub path_clinvar: Vec, + /// ClinVar SV database(s), one for each release. + #[arg(long)] + pub path_clinvar_sv: Vec, + /// CADD database(s), one for each release. + #[arg(long)] + pub path_cadd: Vec, + /// dbSNP database(s), one for each release. + #[arg(long)] + pub path_dbsnp: Vec, + /// dbNSFP database(s), one for each release. + #[arg(long)] + pub path_dbnsfp: Vec, + /// PdbscSNV database(s), one for each release. + #[arg(long)] + pub path_dbscsnv: Vec, + /// gnomAD mtDNA database(s), one for each release. + #[arg(long)] + pub path_gnomad_mtdna: Vec, + /// gnomAD-exomes database(s), one for each release. + #[arg(long)] + pub path_gnomad_exomes: Vec, + /// gnomAD-genomes database(s), one for each release. + #[arg(long)] + pub path_gnomad_genomes: Vec, + /// HelixMtDB database(s), one for each release. + #[arg(long)] + pub path_helixmtdb: Vec, + /// UCSC conservation database(s), one for each release. + #[arg(long)] + pub path_ucsc_conservation: Vec, + + /// IP to listen on. + #[arg(long, default_value = "127.0.0.1")] + pub listen_host: String, + /// Port to listen on. + #[arg(long, default_value_t = 8081)] + pub listen_port: u16, +} + +/// Open a RocksDB database. +/// +/// # Arguments +/// +/// * `path` - Path to the database. +/// * `cf_name` - Name of the column family to open (besides the mandatory `meta` column family). +fn open_db( + path: &str, + cf_name: &str, +) -> Result, anyhow::Error> { + tracing::info!("Opening database {}...", path); + let before_open = Instant::now(); + let res = rocksdb::DB::open_cf_for_read_only( + &rocksdb::Options::default(), + common::readlink_f(path)?, + ["meta", cf_name], + true, + ) + .map_err(|e| anyhow::anyhow!("problem opening database: {}", e)); + tracing::info!("...done opening database in {:?}", before_open.elapsed()); + res +} + +/// Obtain gene names from the genes RocksDB. +fn extract_gene_names( + genes_db: &rocksdb::DBWithThreadMode, +) -> Result, anyhow::Error> { + let mut result = Vec::new(); + + let cf_read = genes_db.cf_handle("genes").unwrap(); + let mut iter = genes_db.raw_iterator_cf(&cf_read); + iter.seek(b""); + while iter.valid() { + if let Some(iter_value) = iter.value() { + let record = genes::base::Record::decode(std::io::Cursor::new(iter_value))?; + let genes::base::Record { hgnc, .. } = record; + if let Some(hgnc) = hgnc { + let genes::base::HgncRecord { + hgnc_id, + symbol, + name, + alias_symbol, + alias_name, + ensembl_gene_id, + entrez_id, + .. + } = hgnc; + result.push(GeneNames { + hgnc_id, + symbol, + name, + alias_symbol, + alias_name, + ensembl_gene_id, + ncbi_gene_id: entrez_id, + }) + } + } + iter.next(); + } + + Ok(result) +} + +/// Main entry point for `server rest` sub command. +pub fn run(args_common: &common::cli::Args, args: &Args) -> Result<(), anyhow::Error> { + 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")); + } + _ => (), + } + } + + tracing::info!("Opening databases..."); + let mut data = WebServerData::default(); + let before_opening = Instant::now(); + + if let Some(path_genes) = args.path_genes.as_ref() { + tracing::info!("Opening genes database {}...", path_genes); + let before_open = Instant::now(); + let db = open_db(path_genes, "genes")?; + tracing::info!( + "...done opening genes database in {:?}", + before_open.elapsed() + ); + + let db_clinvar = if let Some(path_clinvar_genes) = args.path_clinvar_genes.as_ref() { + tracing::info!("Opening ClinVar genes database {}...", path_clinvar_genes); + let before_open = Instant::now(); + let clinvar_db = open_db(path_clinvar_genes, "clinvar-genes")?; + tracing::info!( + "...done opening ClinVar genes database in {:?}", + before_open.elapsed() + ); + Some(clinvar_db) + } else { + None + }; + + tracing::info!("Building gene names..."); + let before_open = Instant::now(); + let gene_names = extract_gene_names(&db)?; + let name_to_hgnc_idx = { + let mut result = HashMap::new(); + for (idx, gene_name) in gene_names.iter().enumerate() { + result.insert(gene_name.hgnc_id.clone(), idx); + if let Some(ensembl_gene_id) = gene_name.ensembl_gene_id.as_ref() { + result.insert(ensembl_gene_id.clone(), idx); + } + if let Some(ncbi_gene_id) = gene_name.ncbi_gene_id.as_ref() { + result.insert(ncbi_gene_id.clone(), idx); + } + result.insert(gene_name.symbol.clone(), idx); + } + result + }; + tracing::info!("...done building genes names {:?}", before_open.elapsed()); + let gene_info_db = GeneInfoDb { + db, + db_clinvar, + gene_names, + name_to_hgnc_idx, + }; + let path_buf = PathBuf::from_str(path_genes)? + .parent() + .ok_or_else(|| anyhow::anyhow!("cannot get parent directory of path {}", path_genes))? + .join("spec.yaml"); + data.genes = Some( + WithVersionSpec::from_data_and_path(gene_info_db, &path_buf).map_err(|e| { + anyhow::anyhow!( + "problem loading gene info spec from {}: {}", + path_buf.display(), + e + ) + })?, + ); + } + + tracing::info!("Opening ClinVar SV databases..."); + let before_clinvar_sv = Instant::now(); + for path_clinvar_sv in &args.path_clinvar_sv { + tracing::info!(" - {}", path_clinvar_sv); + let (clinvar_sv_db, clinvar_sv_meta) = clinvarsv_query::open_rocksdb( + path_clinvar_sv, + "clinvar_sv", + "meta", + "clinvar_sv_by_rcv", + ) + .map_err(|e| anyhow::anyhow!("problem opening RocksDB database: {}", e))?; + let genome_release: GenomeRelease = clinvar_sv_meta.genome_release.parse()?; + tracing::info!(" => {}", genome_release); + let clinvar_sv_interval_trees = + ClinvarsvIntervalTrees::with_db(clinvar_sv_db, "clinvar_sv", clinvar_sv_meta) + .map_err(|e| anyhow::anyhow!("problem building interval trees: {}", e))?; + data.clinvar_svs[genome_release] = Some(clinvar_sv_interval_trees); + } + tracing::info!( + "...done opening ClinVar SV databases in {:?}", + before_clinvar_sv.elapsed() + ); + + // Argument lists from the command line with the corresponding database enum value. + let paths_db_pairs = [ + (&args.path_clinvar, AnnoDb::Clinvar), + (&args.path_cadd, AnnoDb::Cadd), + (&args.path_dbnsfp, AnnoDb::Dbnsfp), + (&args.path_dbsnp, AnnoDb::Dbsnp), + (&args.path_dbscsnv, AnnoDb::Dbscsnv), + (&args.path_gnomad_mtdna, AnnoDb::GnomadMtdna), + (&args.path_gnomad_exomes, AnnoDb::GnomadExomes), + (&args.path_gnomad_genomes, AnnoDb::GnomadGenomes), + (&args.path_helixmtdb, AnnoDb::Helixmtdb), + (&args.path_ucsc_conservation, AnnoDb::UcscConservation), + ]; + // "Unpack" the list of paths to single paths. + let path_db_pairs = paths_db_pairs + .iter() + .map(|(paths, anno_db)| { + paths + .iter() + .map(|path| (path.clone(), *anno_db)) + .collect::>() + }) + .collect::>() + .into_iter() + .flatten() + .collect::>(); + // Open the corresponding databases in parallel and extract database infos. Store the + // resulting database infos in `data`. + path_db_pairs + .par_iter() + .progress_with(crate::common::cli::progress_bar(path_db_pairs.len())) + .map(|(path, anno_db)| -> Result<_, anyhow::Error> { + let db = open_db(path, anno_db.cf_name())?; + let (genome_release, db_info) = fetch_db_info(&db, *anno_db)?; + + Ok((path, db_info, genome_release, db)) + }) + .collect::, _>>()? + .into_iter() + .try_for_each( + |(path_rocksdb, db_info, genome_release, db)| -> Result<(), anyhow::Error> { + let spec_path = PathBuf::from_str(path_rocksdb)? + .parent() + .ok_or_else(|| { + anyhow::anyhow!("cannot get parent directory of path {}", path_rocksdb) + })? + .join("spec.yaml"); + let name = db_info.name; + data.db_infos[genome_release][name] = Some(db_info); + data.annos[genome_release][name] = Some( + WithVersionSpec::from_data_and_path(db, &spec_path).map_err(|e| { + anyhow::anyhow!( + "problem loading gene info spec from {}: {}", + spec_path.display(), + e + ) + })?, + ); + + Ok(()) + }, + )?; + tracing::info!( + "...done opening databases in {:?}", + before_opening.elapsed() + ); + + tracing::info!( + "Launching server main on http://{}:{} ...", + args.listen_host.as_str(), + args.listen_port + ); + tracing::info!( + " try: http://{}:{}/genes/search?q=BRCA", + args.listen_host.as_str(), + args.listen_port + ); + tracing::info!( + " try: http://{}:{}/genes/search?q=BRCA&fields=hgnc_id,ensembl_gene_id,ncbi_gene_id,symbol", + args.listen_host.as_str(), + args.listen_port + ); + tracing::info!( + " try: http://{}:{}/genes/lookup?q=BRCA,BRCA1,HGNC:1100", + args.listen_host.as_str(), + args.listen_port + ); + tracing::info!( + " try: http://{}:{}/genes/info?hgnc_id=HGNC:12403", + args.listen_host.as_str(), + args.listen_port + ); + tracing::info!( + " try: http://{}:{}/genes/clinvar?hgnc_id=HGNC:12403", + args.listen_host.as_str(), + args.listen_port + ); + tracing::info!( + " try: http://{}:{}/annos/db-info?genome_release=grch37", + args.listen_host.as_str(), + args.listen_port + ); + tracing::info!( + " try: http://{}:{}/annos/variant?genome_release=grch37&chromosome=1&pos=55505599&reference=C&alternative=G", + args.listen_host.as_str(), + args.listen_port + ); + tracing::info!( + " try: http://{}:{}/annos/variant?genome_release=grch37&chromosome=1&pos=10001&reference=T&alternative=A", + args.listen_host.as_str(), + args.listen_port + ); + tracing::info!( + " try: http://{}:{}/annos/range?genome_release=grch37&chromosome=1&start=1&stop=55516888", + args.listen_host.as_str(), + args.listen_port + ); + main(args, actix_web::web::Data::new(data))?; + + tracing::info!("All done. Have a nice day!"); + Ok(()) +} diff --git a/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@alphamissense-grch37-1+0.33.0-2.snap b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@alphamissense-grch37-1+0.33.0-2.snap new file mode 100644 index 00000000..dad6968c --- /dev/null +++ b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@alphamissense-grch37-1+0.33.0-2.snap @@ -0,0 +1,20 @@ +--- +source: src/server/run/versions.rs +expression: "&proto_spec" +--- +identifier: "annonars/seqvars/alphamissense:1+0.33.0-grch37" +title: annonars AlphaMissense RocksDB Database +creator: DeepMind +contributor: + - VarFish Developer Teams +format: application/x-rocksdb +date: "20240105" +version: 1+0.33.0 +genomeRelease: grch37 +description: "RocksDB with the information from the AlphaMissense_hgGENOME.tsv.gz\nfiles for the canonical transcripts.\n" +source: + - "PMID:37733863" + - "https://storage.googleapis.com/dm_alphamissense/README.pdf" +createdFrom: + - name: AlphaMissense + version: "1" diff --git a/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@alphamissense-grch37-1+0.33.0.snap b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@alphamissense-grch37-1+0.33.0.snap new file mode 100644 index 00000000..2fc6876c --- /dev/null +++ b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@alphamissense-grch37-1+0.33.0.snap @@ -0,0 +1,20 @@ +--- +source: src/server/run/versions.rs +expression: "&spec" +--- +dc.identifier: "annonars/seqvars/alphamissense:1+0.33.0-grch37" +dc.title: annonars AlphaMissense RocksDB Database +dc.creator: DeepMind +dc.contributor: + - VarFish Developer Teams +dc.format: application/x-rocksdb +dc.date: "20240105" +x-version: 1+0.33.0 +x-genome-release: grch37 +dc.description: "RocksDB with the information from the AlphaMissense_hgGENOME.tsv.gz\nfiles for the canonical transcripts.\n" +dc.source: + - "PMID:37733863" + - "https://storage.googleapis.com/dm_alphamissense/README.pdf" +x-created-from: + - name: AlphaMissense + version: "1" diff --git a/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@alphamissense-grch38-1+0.33.0-2.snap b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@alphamissense-grch38-1+0.33.0-2.snap new file mode 100644 index 00000000..13c0ac54 --- /dev/null +++ b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@alphamissense-grch38-1+0.33.0-2.snap @@ -0,0 +1,20 @@ +--- +source: src/server/run/versions.rs +expression: "&proto_spec" +--- +identifier: "annonars/seqvars/alphamissense:1+0.33.0-grch38" +title: annonars AlphaMissense RocksDB Database +creator: DeepMind +contributor: + - VarFish Developer Teams +format: application/x-rocksdb +date: "20240105" +version: 1+0.33.0 +genomeRelease: grch38 +description: "RocksDB with the information from the AlphaMissense_hgGENOME.tsv.gz\nfiles for the canonical transcripts.\n" +source: + - "PMID:37733863" + - "https://storage.googleapis.com/dm_alphamissense/README.pdf" +createdFrom: + - name: AlphaMissense + version: "1" diff --git a/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@alphamissense-grch38-1+0.33.0.snap b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@alphamissense-grch38-1+0.33.0.snap new file mode 100644 index 00000000..a0e7aaea --- /dev/null +++ b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@alphamissense-grch38-1+0.33.0.snap @@ -0,0 +1,20 @@ +--- +source: src/server/run/versions.rs +expression: "&spec" +--- +dc.identifier: "annonars/seqvars/alphamissense:1+0.33.0-grch38" +dc.title: annonars AlphaMissense RocksDB Database +dc.creator: DeepMind +dc.contributor: + - VarFish Developer Teams +dc.format: application/x-rocksdb +dc.date: "20240105" +x-version: 1+0.33.0 +x-genome-release: grch38 +dc.description: "RocksDB with the information from the AlphaMissense_hgGENOME.tsv.gz\nfiles for the canonical transcripts.\n" +dc.source: + - "PMID:37733863" + - "https://storage.googleapis.com/dm_alphamissense/README.pdf" +x-created-from: + - name: AlphaMissense + version: "1" diff --git a/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@functional-grch37-105.20201022+0.33.0-2.snap b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@functional-grch37-105.20201022+0.33.0-2.snap new file mode 100644 index 00000000..1ab8cf80 --- /dev/null +++ b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@functional-grch37-105.20201022+0.33.0-2.snap @@ -0,0 +1,17 @@ +--- +source: src/server/run/versions.rs +expression: "&proto_spec" +--- +identifier: "annonars/functional:105.20201022+0.33.0-" +title: annonars functional elements RocksDB +creator: VarFish Developer Teams +format: application/x-rocksdb +date: "20240105" +version: 105.20201022+0.33.0 +description: "RocksDB built from RefSeq Functional Elements (and other sources in\nthe future).\n" +source: + - "PMID:34876495" + - "https://www.ncbi.nlm.nih.gov/refseq/" +createdFrom: + - name: RefSeq Functional Elements + version: "105.20201022" diff --git a/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@functional-grch37-105.20201022+0.33.0.snap b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@functional-grch37-105.20201022+0.33.0.snap new file mode 100644 index 00000000..27bd629b --- /dev/null +++ b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@functional-grch37-105.20201022+0.33.0.snap @@ -0,0 +1,17 @@ +--- +source: src/server/run/versions.rs +expression: "&spec" +--- +dc.identifier: "annonars/functional:105.20201022+0.33.0-" +dc.title: annonars functional elements RocksDB +dc.creator: VarFish Developer Teams +dc.format: application/x-rocksdb +dc.date: "20240105" +x-version: 105.20201022+0.33.0 +dc.description: "RocksDB built from RefSeq Functional Elements (and other sources in\nthe future).\n" +dc.source: + - "PMID:34876495" + - "https://www.ncbi.nlm.nih.gov/refseq/" +x-created-from: + - name: RefSeq Functional Elements + version: "105.20201022" diff --git a/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@functional-grch38-110+0.33.0-2.snap b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@functional-grch38-110+0.33.0-2.snap new file mode 100644 index 00000000..9db8eff2 --- /dev/null +++ b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@functional-grch38-110+0.33.0-2.snap @@ -0,0 +1,17 @@ +--- +source: src/server/run/versions.rs +expression: "&proto_spec" +--- +identifier: "annonars/functional:110+0.33.0-" +title: annonars functional elements RocksDB +creator: VarFish Developer Teams +format: application/x-rocksdb +date: "20240105" +version: 110+0.33.0 +description: "RocksDB built from RefSeq Functional Elements (and other sources in\nthe future).\n" +source: + - "PMID:34876495" + - "https://www.ncbi.nlm.nih.gov/refseq/" +createdFrom: + - name: RefSeq Functional Elements + version: "110" diff --git a/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@functional-grch38-110+0.33.0.snap b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@functional-grch38-110+0.33.0.snap new file mode 100644 index 00000000..ea194df5 --- /dev/null +++ b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@functional-grch38-110+0.33.0.snap @@ -0,0 +1,17 @@ +--- +source: src/server/run/versions.rs +expression: "&spec" +--- +dc.identifier: "annonars/functional:110+0.33.0-" +dc.title: annonars functional elements RocksDB +dc.creator: VarFish Developer Teams +dc.format: application/x-rocksdb +dc.date: "20240105" +x-version: 110+0.33.0 +dc.description: "RocksDB built from RefSeq Functional Elements (and other sources in\nthe future).\n" +dc.source: + - "PMID:34876495" + - "https://www.ncbi.nlm.nih.gov/refseq/" +x-created-from: + - name: RefSeq Functional Elements + version: "110" diff --git a/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@genes-3.1+4.0+4.5+20230606+10.1+20240105+0.33.0-2.snap b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@genes-3.1+4.0+4.5+20230606+10.1+20240105+0.33.0-2.snap new file mode 100644 index 00000000..35a3abe1 --- /dev/null +++ b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@genes-3.1+4.0+4.5+20230606+10.1+20240105+0.33.0-2.snap @@ -0,0 +1,43 @@ +--- +source: src/server/run/versions.rs +expression: "&proto_spec" +--- +identifier: "annonars/genes:3.1+4.0+4.5+20240105+0.33.0" +title: annonars genes database +creator: VarFish Development Team +format: application/x-rocksdb +date: "20240105" +version: 3.1+4.0+4.5+20240105+0.33.0 +description: "Gene information from the following databases, aggregated using annonars\nv0.33.0 in varfish-downloader v0.3.1.dev42+g3a332a0.d20240105:\n\n- ACMG Supplementary Findings Gene List 3.1\n- gnomAD constraints v4.0\n- dbNSFP v4.5\n- NCBI gene database downloaded at 20240105\n- HGNC database downloaded at 20240105\n- ClinGen Gene Dosage pathogenicity 20240105\n- DOMINO data v2019-02-19\n" +source: + - "PMID:35802134" + - "PMID:32461654" + - "PMID:33261662" + - "PMID:28985496" + - "https://www.ncbi.nlm.nih.gov/gene/" + - "https://www.genenames.org/" +createdFrom: + - name: ACMG SF Gene List + version: "3.1" + - name: ClinGen Gene Dosage pathog + version: "20240105" + - name: gnomAD constraints + version: "4.0" + - name: dbNSFP + version: "4.5" + - name: NCBI gene + version: "20240105" + - name: HGNC + version: "20240105" + - name: OMIM + version: "20240105" + - name: ORDO + version: "10.1" + - name: rCNV pHaplo/pTriplo scores + version: 2022-Collins-et-al + - name: sHet scores + version: 2019-Weghorn-et-a. + - name: GTex data + version: v8 + - name: DOMINO data + version: 2019-02-19 diff --git a/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@genes-3.1+4.0+4.5+20230606+10.1+20240105+0.33.0.snap b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@genes-3.1+4.0+4.5+20230606+10.1+20240105+0.33.0.snap new file mode 100644 index 00000000..91209dd7 --- /dev/null +++ b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@genes-3.1+4.0+4.5+20230606+10.1+20240105+0.33.0.snap @@ -0,0 +1,43 @@ +--- +source: src/server/run/versions.rs +expression: "&spec" +--- +dc.identifier: "annonars/genes:3.1+4.0+4.5+20240105+0.33.0" +dc.title: annonars genes database +dc.creator: VarFish Development Team +dc.format: application/x-rocksdb +dc.date: "20240105" +x-version: 3.1+4.0+4.5+20240105+0.33.0 +dc.description: "Gene information from the following databases, aggregated using annonars\nv0.33.0 in varfish-downloader v0.3.1.dev42+g3a332a0.d20240105:\n\n- ACMG Supplementary Findings Gene List 3.1\n- gnomAD constraints v4.0\n- dbNSFP v4.5\n- NCBI gene database downloaded at 20240105\n- HGNC database downloaded at 20240105\n- ClinGen Gene Dosage pathogenicity 20240105\n- DOMINO data v2019-02-19\n" +dc.source: + - "PMID:35802134" + - "PMID:32461654" + - "PMID:33261662" + - "PMID:28985496" + - "https://www.ncbi.nlm.nih.gov/gene/" + - "https://www.genenames.org/" +x-created-from: + - name: ACMG SF Gene List + version: "3.1" + - name: ClinGen Gene Dosage pathog + version: "20240105" + - name: gnomAD constraints + version: "4.0" + - name: dbNSFP + version: "4.5" + - name: NCBI gene + version: "20240105" + - name: HGNC + version: "20240105" + - name: OMIM + version: "20240105" + - name: ORDO + version: "10.1" + - name: rCNV pHaplo/pTriplo scores + version: 2022-Collins-et-al + - name: sHet scores + version: 2019-Weghorn-et-a. + - name: GTex data + version: v8 + - name: DOMINO data + version: 2019-02-19 diff --git a/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@gnomad-mtdna-grch37-3.1+0.33.0-2.snap b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@gnomad-mtdna-grch37-3.1+0.33.0-2.snap new file mode 100644 index 00000000..bfdf475f --- /dev/null +++ b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@gnomad-mtdna-grch37-3.1+0.33.0-2.snap @@ -0,0 +1,20 @@ +--- +source: src/server/run/versions.rs +expression: "&proto_spec" +--- +identifier: "annonars/seqvars/gnomad-mtdna:3.1+0.33.0-grch37" +title: annonars gnomAD-mtDNA RocksDB Database +creator: gnomAD Team +contributor: + - VarFish Developer Teams +format: application/x-rocksdb +date: "20240105" +version: 3.1+0.33.0 +genomeRelease: grch37 +description: "RocksDB with the information from gnomAD mtDNA v3.1 converted with\nannonars v0.33.0 in varfish-downloader v0.3.1.dev42+g3a332a0.d20240105.\n" +source: + - "PMID:32461654" + - "https://gnomad.broadinstitute.org/" +createdFrom: + - name: gnomAD-mtDNA + version: "3.1" diff --git a/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@gnomad-mtdna-grch37-3.1+0.33.0.snap b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@gnomad-mtdna-grch37-3.1+0.33.0.snap new file mode 100644 index 00000000..1807e130 --- /dev/null +++ b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@gnomad-mtdna-grch37-3.1+0.33.0.snap @@ -0,0 +1,20 @@ +--- +source: src/server/run/versions.rs +expression: "&spec" +--- +dc.identifier: "annonars/seqvars/gnomad-mtdna:3.1+0.33.0-grch37" +dc.title: annonars gnomAD-mtDNA RocksDB Database +dc.creator: gnomAD Team +dc.contributor: + - VarFish Developer Teams +dc.format: application/x-rocksdb +dc.date: "20240105" +x-version: 3.1+0.33.0 +x-genome-release: grch37 +dc.description: "RocksDB with the information from gnomAD mtDNA v3.1 converted with\nannonars v0.33.0 in varfish-downloader v0.3.1.dev42+g3a332a0.d20240105.\n" +dc.source: + - "PMID:32461654" + - "https://gnomad.broadinstitute.org/" +x-created-from: + - name: gnomAD-mtDNA + version: "3.1" diff --git a/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@gnomad-mtdna-grch38-3.1+0.33.0-2.snap b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@gnomad-mtdna-grch38-3.1+0.33.0-2.snap new file mode 100644 index 00000000..c82a4bc0 --- /dev/null +++ b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@gnomad-mtdna-grch38-3.1+0.33.0-2.snap @@ -0,0 +1,20 @@ +--- +source: src/server/run/versions.rs +expression: "&proto_spec" +--- +identifier: "annonars/seqvars/gnomad-mtdna:3.1+0.33.0-grch38" +title: annonars gnomAD-mtDNA RocksDB Database +creator: gnomAD Team +contributor: + - VarFish Developer Teams +format: application/x-rocksdb +date: "20240105" +version: 3.1+0.33.0 +genomeRelease: grch38 +description: "RocksDB with the information from gnomAD mtDNA v3.1 converted with\nannonars v0.33.0 in varfish-downloader v0.3.1.dev42+g3a332a0.d20240105.\n" +source: + - "PMID:32461654" + - "https://gnomad.broadinstitute.org/" +createdFrom: + - name: gnomAD-mtDNA + version: "3.1" diff --git a/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@gnomad-mtdna-grch38-3.1+0.33.0.snap b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@gnomad-mtdna-grch38-3.1+0.33.0.snap new file mode 100644 index 00000000..f5223741 --- /dev/null +++ b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@gnomad-mtdna-grch38-3.1+0.33.0.snap @@ -0,0 +1,20 @@ +--- +source: src/server/run/versions.rs +expression: "&spec" +--- +dc.identifier: "annonars/seqvars/gnomad-mtdna:3.1+0.33.0-grch38" +dc.title: annonars gnomAD-mtDNA RocksDB Database +dc.creator: gnomAD Team +dc.contributor: + - VarFish Developer Teams +dc.format: application/x-rocksdb +dc.date: "20240105" +x-version: 3.1+0.33.0 +x-genome-release: grch38 +dc.description: "RocksDB with the information from gnomAD mtDNA v3.1 converted with\nannonars v0.33.0 in varfish-downloader v0.3.1.dev42+g3a332a0.d20240105.\n" +dc.source: + - "PMID:32461654" + - "https://gnomad.broadinstitute.org/" +x-created-from: + - name: gnomAD-mtDNA + version: "3.1" diff --git a/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@helixmtdb-grch37-20200327+0.33.0-2.snap b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@helixmtdb-grch37-20200327+0.33.0-2.snap new file mode 100644 index 00000000..2deca7b0 --- /dev/null +++ b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@helixmtdb-grch37-20200327+0.33.0-2.snap @@ -0,0 +1,19 @@ +--- +source: src/server/run/versions.rs +expression: "&proto_spec" +--- +identifier: "annonars/seqvars/helixmtdb:20200327+0.33.0-grch37" +title: annonars HelixMtDb RocksDB Database +creator: "Helix OpCo, LLC" +contributor: + - VarFish Developer Teams +format: application/x-rocksdb +date: "20240105" +version: 20200327+0.33.0 +genomeRelease: grch37 +description: "RocksDB with the information from HelixMtDb v20200327 imported using\nthe annonars package v0.33.0 in varfish-downloader\nv0.3.1.dev42+g3a332a0.d20240105.\n" +source: + - "https://www.helix.com/pages/mitochondrial-variant-database" +createdFrom: + - name: HelixMtdB + version: "20200327" diff --git a/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@helixmtdb-grch37-20200327+0.33.0.snap b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@helixmtdb-grch37-20200327+0.33.0.snap new file mode 100644 index 00000000..9280d79a --- /dev/null +++ b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@helixmtdb-grch37-20200327+0.33.0.snap @@ -0,0 +1,19 @@ +--- +source: src/server/run/versions.rs +expression: "&spec" +--- +dc.identifier: "annonars/seqvars/helixmtdb:20200327+0.33.0-grch37" +dc.title: annonars HelixMtDb RocksDB Database +dc.creator: "Helix OpCo, LLC" +dc.contributor: + - VarFish Developer Teams +dc.format: application/x-rocksdb +dc.date: "20240105" +x-version: 20200327+0.33.0 +x-genome-release: grch37 +dc.description: "RocksDB with the information from HelixMtDb v20200327 imported using\nthe annonars package v0.33.0 in varfish-downloader\nv0.3.1.dev42+g3a332a0.d20240105.\n" +dc.source: + - "https://www.helix.com/pages/mitochondrial-variant-database" +x-created-from: + - name: HelixMtdB + version: "20200327" diff --git a/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@helixmtdb-grch38-20200327+0.33.0-2.snap b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@helixmtdb-grch38-20200327+0.33.0-2.snap new file mode 100644 index 00000000..5157c4c9 --- /dev/null +++ b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@helixmtdb-grch38-20200327+0.33.0-2.snap @@ -0,0 +1,19 @@ +--- +source: src/server/run/versions.rs +expression: "&proto_spec" +--- +identifier: "annonars/seqvars/helixmtdb:20200327+0.33.0-grch38" +title: annonars HelixMtDb RocksDB Database +creator: "Helix OpCo, LLC" +contributor: + - VarFish Developer Teams +format: application/x-rocksdb +date: "20240105" +version: 20200327+0.33.0 +genomeRelease: grch38 +description: "RocksDB with the information from HelixMtDb v20200327 imported using\nthe annonars package v0.33.0 in varfish-downloader\nv0.3.1.dev42+g3a332a0.d20240105.\n" +source: + - "https://www.helix.com/pages/mitochondrial-variant-database" +createdFrom: + - name: HelixMtdB + version: "20200327" diff --git a/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@helixmtdb-grch38-20200327+0.33.0.snap b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@helixmtdb-grch38-20200327+0.33.0.snap new file mode 100644 index 00000000..ec73895d --- /dev/null +++ b/src/server/run/snapshots/annonars__server__run__versions__test__deserialize_spec_yaml@helixmtdb-grch38-20200327+0.33.0.snap @@ -0,0 +1,19 @@ +--- +source: src/server/run/versions.rs +expression: "&spec" +--- +dc.identifier: "annonars/seqvars/helixmtdb:20200327+0.33.0-grch38" +dc.title: annonars HelixMtDb RocksDB Database +dc.creator: "Helix OpCo, LLC" +dc.contributor: + - VarFish Developer Teams +dc.format: application/x-rocksdb +dc.date: "20240105" +x-version: 20200327+0.33.0 +x-genome-release: grch38 +dc.description: "RocksDB with the information from HelixMtDb v20200327 imported using\nthe annonars package v0.33.0 in varfish-downloader\nv0.3.1.dev42+g3a332a0.d20240105.\n" +dc.source: + - "https://www.helix.com/pages/mitochondrial-variant-database" +x-created-from: + - name: HelixMtdB + version: "20200327" diff --git a/src/server/run/versions.rs b/src/server/run/versions.rs new file mode 100644 index 00000000..683c02bf --- /dev/null +++ b/src/server/run/versions.rs @@ -0,0 +1,227 @@ +//! Provide information about the software and database versions. + +use actix_web::{ + get, + web::{self, Data, Json, Path}, + Responder, +}; + +use crate::{common::cli::GenomeRelease, pbs::common::versions::VersionSpec}; + +use super::{error::CustomError, AnnoDb, WebServerData}; + +/// Code for deserializing the version `spec.yaml` files. +pub mod schema { + use std::path::Path; + + use crate::pbs; + + /// Information about input data. + #[derive(serde::Deserialize, serde::Serialize, Debug, Clone)] + pub struct CreatedFrom { + /// Data source name. + pub name: String, + /// Version of the data source. + pub version: String, + } + + impl Into for CreatedFrom { + fn into(self) -> pbs::common::versions::CreatedFrom { + let Self { name, version } = self; + pbs::common::versions::CreatedFrom { name, version } + } + } + + /// Version specification. + #[serde_with::skip_serializing_none] + #[serde_with::serde_as] + #[derive(serde::Deserialize, serde::Serialize, Debug, Clone)] + pub struct VersionSpec { + /// Identifier of the data. + #[serde(rename = "dc.identifier")] + pub identifier: String, + /// Title of the data. + #[serde(rename = "dc.title")] + pub title: String, + /// Creator of the data. + #[serde(rename = "dc.creator")] + pub creator: String, + /// Contributors of the data. + #[serde(rename = "dc.contributor")] + pub contributor: Option>, + /// Format of the data. + #[serde(rename = "dc.format")] + pub format: String, + /// Date of the data. + #[serde(rename = "dc.date")] + pub date: String, + /// Version of the data. + #[serde(rename = "x-version")] + pub version: String, + /// Optional genome release. + #[serde(rename = "x-genome-release")] + pub genome_release: Option, + /// Data description. + #[serde(rename = "dc.description")] + pub description: String, + /// Data source. + #[serde(rename = "dc.source")] + pub source: Vec, + /// Created from information. + #[serde(rename = "x-created-from")] + pub created_from: Vec, + } + + impl VersionSpec { + /// Read a `VersionSpec` from a YAML file. + pub fn from_path

(p: P) -> Result + where + P: AsRef, + { + let full_path = p.as_ref().to_str().ok_or_else(|| { + anyhow::anyhow!("problem converting path to string: {:?}", p.as_ref()) + })?; + let yaml_str = std::fs::read_to_string(&full_path) + .map_err(|e| anyhow::anyhow!("problem reading file {}: {}", &full_path, e))?; + serde_yaml::from_str(&yaml_str) + .map_err(|e| anyhow::anyhow!("problem deserializing {}: {}", full_path, e)) + } + } + + impl Into for VersionSpec { + fn into(self) -> pbs::common::versions::VersionSpec { + let Self { + identifier, + title, + creator, + contributor, + format, + date, + version, + genome_release, + description, + source, + created_from, + } = self; + pbs::common::versions::VersionSpec { + identifier, + title, + creator, + contributor: contributor.unwrap_or_default(), + format, + date, + version, + genome_release, + description, + source, + created_from: created_from.into_iter().map(Into::into).collect(), + } + } + } +} + +/// Query parameters for `handle()`. +#[derive(Debug, Clone, serde::Deserialize, utoipa::IntoParams)] +pub struct VersionInfoQuery {} + +/// Version information for one database. +#[derive(Debug, Clone, serde::Serialize, utoipa::ToSchema)] +#[serde(rename_all = "camelCase")] +pub struct AnnoVersionInfo { + /// Database name. + pub database: AnnoDb, + /// Version information of the database. + pub version_spec: VersionSpec, +} + +/// Version information for databases in a given release. +#[derive(Debug, Default, Clone, serde::Serialize, utoipa::ToSchema)] +#[serde(rename_all = "camelCase")] +pub struct ReleaseVersionInfos { + /// The genome release. + pub release: GenomeRelease, + /// Version information of annotation databases. + #[serde(skip_serializing_if = "Vec::is_empty")] + pub version_infos: Vec, +} + +/// Response for `handle()`. +#[derive(Debug, Default, Clone, serde::Serialize, utoipa::ToSchema)] +pub struct VersionInfoResponse { + /// Version information of the genes. + #[serde(skip_serializing_if = "Option::is_none")] + pub genes: Option, + /// Version information of annotation databases per release. + #[serde(skip_serializing_if = "Vec::is_empty")] + pub annos: Vec, +} + +/// Query for annotations for one variant. +#[utoipa::path( + get, + operation_id = "versionInfos", + params(VersionInfoQuery), + responses( + (status = 200, description = "Version information.", body = VersionInfoResponse), + ) +)] +#[get("/v1/versions")] +async fn handle( + data: Data, + _path: Path<()>, + _query: web::Query, +) -> actix_web::Result { + let mut annos = Vec::new(); + for (release, anno_dbs) in data.as_ref().annos.iter() { + let mut version_infos = Vec::new(); + for (anno_db, with_version) in anno_dbs { + if let Some(with_version) = with_version.as_ref() { + version_infos.push(AnnoVersionInfo { + database: anno_db.clone(), + version_spec: with_version.version_spec.clone().into(), + }); + } + } + annos.push(ReleaseVersionInfos { + release, + version_infos, + }); + } + + let response = VersionInfoResponse { + genes: data + .as_ref() + .genes + .as_ref() + .map(|genes| genes.version_spec.clone()), + annos, + }; + + Ok(Json(response)) +} + +#[cfg(test)] +pub mod test { + #[rstest::rstest] + #[case("alphamissense-grch37-1+0.33.0")] + #[case("alphamissense-grch38-1+0.33.0")] + #[case("functional-grch37-105.20201022+0.33.0")] + #[case("functional-grch38-110+0.33.0")] + #[case("genes-3.1+4.0+4.5+20230606+10.1+20240105+0.33.0")] + #[case("gnomad-mtdna-grch37-3.1+0.33.0")] + #[case("gnomad-mtdna-grch38-3.1+0.33.0")] + #[case("helixmtdb-grch37-20200327+0.33.0")] + #[case("helixmtdb-grch38-20200327+0.33.0")] + fn test_deserialize_spec_yaml(#[case] name: &str) -> Result<(), anyhow::Error> { + crate::common::set_snapshot_suffix!("{}", &name); + + let full_path = format!("tests/server/annonars/{}/spec.yaml", &name); + let spec = super::schema::VersionSpec::from_path(&full_path)?; + insta::assert_yaml_snapshot!(&spec); + + let proto_spec: crate::pbs::common::versions::VersionSpec = spec.into(); + insta::assert_yaml_snapshot!(&proto_spec); + + Ok(()) + } +} diff --git a/src/server/schema.rs b/src/server/schema.rs new file mode 100644 index 00000000..feedc03f --- /dev/null +++ b/src/server/schema.rs @@ -0,0 +1,51 @@ +//! Dump schema of the REST API server. + +use std::{ + fs::File, + io::{self, Write}, +}; + +use utoipa::OpenApi as _; + +use crate::server::run::openapi::ApiDoc; + +/// Command line arguments for `server schema` sub command. +#[derive(clap::Parser, Debug, Clone)] +#[command(author, version, about = "Dump REST API schema", long_about = None)] +pub struct Args { + /// Path to the output file. Use stdout if missing. + #[arg(long)] + pub output_file: Option, +} + +impl Args { + /// Get writeable output file or stdout. + fn get_output(&self) -> Result, io::Error> { + match self.output_file { + Some(ref path) => File::create(path).map(|f| Box::new(f) as Box), + None => Ok(Box::new(io::stdout())), + } + } +} + +/// Main entry point for `run-server` sub command. +/// +/// # Errors +/// +/// In the case that there is an error running the server. +pub fn run(args_common: &crate::common::cli::Args, args: &Args) -> Result<(), anyhow::Error> { + tracing::info!("args_common = {:?}", &args_common); + tracing::info!("args = {:?}", &args); + + let schema_yaml = ApiDoc::openapi() + .to_yaml() + .map_err(|e| anyhow::anyhow!("Failed to convert OpenAPI to YAML: {}", e))?; + let mut output = args + .get_output() + .map_err(|e| anyhow::anyhow!("Failed to open output file: {}", e))?; + write!(output, "{}", &schema_yaml) + .map_err(|e| anyhow::anyhow!("Failed to write output: {}", e))?; + + tracing::info!("All done. Have a nice day!"); + Ok(()) +} diff --git a/tests/server/annonars/alphamissense-grch37-1+0.33.0/MANIFEST.txt b/tests/server/annonars/alphamissense-grch37-1+0.33.0/MANIFEST.txt new file mode 100644 index 00000000..d62db90f --- /dev/null +++ b/tests/server/annonars/alphamissense-grch37-1+0.33.0/MANIFEST.txt @@ -0,0 +1,17 @@ +## Invoked from: /data/cephfs-1/work/projects/cubi-varfish-data/2023-06-05_varfish-db-downloader/varfish-db-downloader/output/full/annonars/alphamissense-grch37-1+0.33.0 +## $ hashdeep -l -r . +## +%%%% HASHDEEP-1.0 +1640,90471bc5dec37e70b55bed6bc18051b4,b9fc31aefe9883259e455c57109b6fe10b1c9eef1f0114bbc15c415f4fd5fd76,./rocksdb/000032.sst +16,1499571836189b80bb3138a553dbd79a,306d61aa07213eb5ff589100ad05aedf9b844bccec89d638b94259494e54d751,./rocksdb/CURRENT +36,5e2976068d2a75d53d0ff09d6f08333b,15cd1ee707783a75a1aa3b5917e4213d96b297b8c7d583ae90cd3d0ad350c1b9,./rocksdb/IDENTITY +0,d41d8cd98f00b204e9800998ecf8427e,e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855,./rocksdb/LOCK +58842,e6c6b09f6f0272c990c918bfd08f795e,88c9981891bcf8efef358071aab967fcf18ef6b28e0d3c074862ef4c7d18b1d3,./rocksdb/LOG +58000,247ee11ce579e1208b9e3e2f2fa076f1,fb8ed753fe371cc359406aa8947fc39281de6919bc29de6f0b71e8cf58b13031,./rocksdb/LOG.old.1704452449494627 +58838,09c062bd6c8567f9c36206da7a100149,59eca4c0ab6787d390487fcb79600a50a4fc6109013745d9e38a9c0f547efc78,./rocksdb/LOG.old.1704453775733287 +558,f59730c76ac5a679fa338b8edec4d769,7d646655ac7b5f74c445e1f80a7bfbf5606df8345b2399b27b45e6bc3b6ca1b6,./rocksdb/MANIFEST-000027 +15359,d61627a598dfdde2fcb566e58382cbc7,171451321c4f9689cb7edbe4be4c16d7e3bd30bc12923a20def2dd7fad5b32ca,./rocksdb/OPTIONS-000020 +15359,d61627a598dfdde2fcb566e58382cbc7,171451321c4f9689cb7edbe4be4c16d7e3bd30bc12923a20def2dd7fad5b32ca,./rocksdb/OPTIONS-000029 +547,14a5245a011dc50699574c983ba4b5ac,38d7bf1883c862a8f0546708e89858279cf289d41680bfcbbc8b459533103e88,./spec.yaml +%%%% size,md5,sha256,filename +## EOF SHA256=4e0580c847d8411ff5b909c082c3cf7e1102d5ce497de50a79a0b0a850e440d2 diff --git a/tests/server/annonars/alphamissense-grch37-1+0.33.0/rocksdb/000032.sst b/tests/server/annonars/alphamissense-grch37-1+0.33.0/rocksdb/000032.sst new file mode 100644 index 00000000..46f598f1 --- /dev/null +++ b/tests/server/annonars/alphamissense-grch37-1+0.33.0/rocksdb/000032.sst @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b9fc31aefe9883259e455c57109b6fe10b1c9eef1f0114bbc15c415f4fd5fd76 +size 1640 diff --git a/tests/server/annonars/alphamissense-grch37-1+0.33.0/rocksdb/CURRENT b/tests/server/annonars/alphamissense-grch37-1+0.33.0/rocksdb/CURRENT new file mode 100644 index 00000000..18fee780 --- /dev/null +++ b/tests/server/annonars/alphamissense-grch37-1+0.33.0/rocksdb/CURRENT @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:306d61aa07213eb5ff589100ad05aedf9b844bccec89d638b94259494e54d751 +size 16 diff --git a/tests/server/annonars/alphamissense-grch37-1+0.33.0/rocksdb/IDENTITY b/tests/server/annonars/alphamissense-grch37-1+0.33.0/rocksdb/IDENTITY new file mode 100644 index 00000000..80deca7b --- /dev/null +++ b/tests/server/annonars/alphamissense-grch37-1+0.33.0/rocksdb/IDENTITY @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:15cd1ee707783a75a1aa3b5917e4213d96b297b8c7d583ae90cd3d0ad350c1b9 +size 36 diff --git a/tests/server/annonars/alphamissense-grch37-1+0.33.0/rocksdb/LOCK b/tests/server/annonars/alphamissense-grch37-1+0.33.0/rocksdb/LOCK new file mode 100644 index 00000000..e69de29b diff --git a/tests/server/annonars/alphamissense-grch37-1+0.33.0/rocksdb/LOG b/tests/server/annonars/alphamissense-grch37-1+0.33.0/rocksdb/LOG new file mode 100644 index 00000000..0506a801 --- /dev/null +++ b/tests/server/annonars/alphamissense-grch37-1+0.33.0/rocksdb/LOG @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:88c9981891bcf8efef358071aab967fcf18ef6b28e0d3c074862ef4c7d18b1d3 +size 58842 diff --git a/tests/server/annonars/alphamissense-grch37-1+0.33.0/rocksdb/LOG.old.1704452449494627 b/tests/server/annonars/alphamissense-grch37-1+0.33.0/rocksdb/LOG.old.1704452449494627 new file mode 100644 index 00000000..712eb595 --- /dev/null +++ b/tests/server/annonars/alphamissense-grch37-1+0.33.0/rocksdb/LOG.old.1704452449494627 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:fb8ed753fe371cc359406aa8947fc39281de6919bc29de6f0b71e8cf58b13031 +size 58000 diff --git a/tests/server/annonars/alphamissense-grch37-1+0.33.0/rocksdb/LOG.old.1704453775733287 b/tests/server/annonars/alphamissense-grch37-1+0.33.0/rocksdb/LOG.old.1704453775733287 new file mode 100644 index 00000000..f01bc63b --- /dev/null +++ b/tests/server/annonars/alphamissense-grch37-1+0.33.0/rocksdb/LOG.old.1704453775733287 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:59eca4c0ab6787d390487fcb79600a50a4fc6109013745d9e38a9c0f547efc78 +size 58838 diff --git a/tests/server/annonars/alphamissense-grch37-1+0.33.0/rocksdb/MANIFEST-000027 b/tests/server/annonars/alphamissense-grch37-1+0.33.0/rocksdb/MANIFEST-000027 new file mode 100644 index 00000000..6b88c70a --- /dev/null +++ b/tests/server/annonars/alphamissense-grch37-1+0.33.0/rocksdb/MANIFEST-000027 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:7d646655ac7b5f74c445e1f80a7bfbf5606df8345b2399b27b45e6bc3b6ca1b6 +size 558 diff --git a/tests/server/annonars/alphamissense-grch37-1+0.33.0/rocksdb/OPTIONS-000020 b/tests/server/annonars/alphamissense-grch37-1+0.33.0/rocksdb/OPTIONS-000020 new file mode 100644 index 00000000..ac5c0fe8 --- /dev/null +++ b/tests/server/annonars/alphamissense-grch37-1+0.33.0/rocksdb/OPTIONS-000020 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:171451321c4f9689cb7edbe4be4c16d7e3bd30bc12923a20def2dd7fad5b32ca +size 15359 diff --git a/tests/server/annonars/alphamissense-grch37-1+0.33.0/rocksdb/OPTIONS-000029 b/tests/server/annonars/alphamissense-grch37-1+0.33.0/rocksdb/OPTIONS-000029 new file mode 100644 index 00000000..ac5c0fe8 --- /dev/null +++ b/tests/server/annonars/alphamissense-grch37-1+0.33.0/rocksdb/OPTIONS-000029 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:171451321c4f9689cb7edbe4be4c16d7e3bd30bc12923a20def2dd7fad5b32ca +size 15359 diff --git a/tests/server/annonars/alphamissense-grch37-1+0.33.0/spec.yaml b/tests/server/annonars/alphamissense-grch37-1+0.33.0/spec.yaml new file mode 100644 index 00000000..2e19a308 --- /dev/null +++ b/tests/server/annonars/alphamissense-grch37-1+0.33.0/spec.yaml @@ -0,0 +1,18 @@ +dc.identifier: annonars/seqvars/alphamissense:1+0.33.0-grch37 +dc.title: annonars AlphaMissense RocksDB Database +dc.creator: DeepMind +dc.contributor: + - VarFish Developer Teams +dc.format: application/x-rocksdb +dc.date: 20240105 +x-version: 1+0.33.0 +x-genome-release: grch37 +dc.description: | + RocksDB with the information from the AlphaMissense_hgGENOME.tsv.gz + files for the canonical transcripts. +dc.source: + - PMID:37733863 + - https://storage.googleapis.com/dm_alphamissense/README.pdf +x-created-from: + - name: AlphaMissense + version: 1 diff --git a/tests/server/annonars/alphamissense-grch37-1+0.39.0/rocksdb/000010.sst b/tests/server/annonars/alphamissense-grch37-1+0.39.0/rocksdb/000010.sst new file mode 100644 index 00000000..83e10444 --- /dev/null +++ b/tests/server/annonars/alphamissense-grch37-1+0.39.0/rocksdb/000010.sst @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:642c288b3ec70c8cd55e4d4659f6fedbaa40deafed2c3fff0ee1b8fc086b8c74 +size 1662 diff --git a/tests/server/annonars/alphamissense-grch37-1+0.39.0/rocksdb/CURRENT b/tests/server/annonars/alphamissense-grch37-1+0.39.0/rocksdb/CURRENT new file mode 100644 index 00000000..f8d50486 --- /dev/null +++ b/tests/server/annonars/alphamissense-grch37-1+0.39.0/rocksdb/CURRENT @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:9c283f6e81028b9eb0760d918ee4bc0aa256ed3b926393c1734c760c4bd724fd +size 16 diff --git a/tests/server/annonars/alphamissense-grch37-1+0.39.0/rocksdb/IDENTITY b/tests/server/annonars/alphamissense-grch37-1+0.39.0/rocksdb/IDENTITY new file mode 100644 index 00000000..1587d0e6 --- /dev/null +++ b/tests/server/annonars/alphamissense-grch37-1+0.39.0/rocksdb/IDENTITY @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a11d185b17370335983f1decb531aebe8c45a46a157566887f70551425c025cb +size 36 diff --git a/tests/server/annonars/alphamissense-grch37-1+0.39.0/rocksdb/LOCK b/tests/server/annonars/alphamissense-grch37-1+0.39.0/rocksdb/LOCK new file mode 100644 index 00000000..e69de29b diff --git a/tests/server/annonars/alphamissense-grch37-1+0.39.0/rocksdb/LOG b/tests/server/annonars/alphamissense-grch37-1+0.39.0/rocksdb/LOG new file mode 100644 index 00000000..c63896cc --- /dev/null +++ b/tests/server/annonars/alphamissense-grch37-1+0.39.0/rocksdb/LOG @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6cf2b8f5a854d44753caeefb29df88f0fd8975b8f222787a118dbe51e3f3cce9 +size 59313 diff --git a/tests/server/annonars/alphamissense-grch37-1+0.39.0/rocksdb/MANIFEST-000005 b/tests/server/annonars/alphamissense-grch37-1+0.39.0/rocksdb/MANIFEST-000005 new file mode 100644 index 00000000..79f052ec --- /dev/null +++ b/tests/server/annonars/alphamissense-grch37-1+0.39.0/rocksdb/MANIFEST-000005 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:85879395273c368f6faf37f3f7461ece3144a6bbbb09ee09e9a55165833d2049 +size 448 diff --git a/tests/server/annonars/alphamissense-grch37-1+0.39.0/rocksdb/OPTIONS-000007 b/tests/server/annonars/alphamissense-grch37-1+0.39.0/rocksdb/OPTIONS-000007 new file mode 100644 index 00000000..0a7b04f0 --- /dev/null +++ b/tests/server/annonars/alphamissense-grch37-1+0.39.0/rocksdb/OPTIONS-000007 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:af00ab6ac001ddbf1487a535f5681e84465c394a69c4f559b1198ae013603a36 +size 16308 diff --git a/tests/server/annonars/alphamissense-grch37-1+0.39.0/spec.yaml b/tests/server/annonars/alphamissense-grch37-1+0.39.0/spec.yaml new file mode 100644 index 00000000..dee78633 --- /dev/null +++ b/tests/server/annonars/alphamissense-grch37-1+0.39.0/spec.yaml @@ -0,0 +1,18 @@ +dc.identifier: annonars/seqvars/alphamissense:1+0.39.0-grch37 +dc.title: annonars AlphaMissense RocksDB Database +dc.creator: DeepMind +dc.contributor: + - VarFish Developer Teams +dc.format: application/x-rocksdb +dc.date: 20240711 +x-version: 1+0.39.0 +x-genome-release: grch37 +dc.description: | + RocksDB with the information from the AlphaMissense_hgGENOME.tsv.gz + files for the canonical transcripts. +dc.source: + - PMID:37733863 + - https://storage.googleapis.com/dm_alphamissense/README.pdf +x-created-from: + - name: AlphaMissense + version: 1 diff --git a/tests/server/annonars/alphamissense-grch38-1+0.33.0/MANIFEST.txt b/tests/server/annonars/alphamissense-grch38-1+0.33.0/MANIFEST.txt new file mode 100644 index 00000000..197244dc --- /dev/null +++ b/tests/server/annonars/alphamissense-grch38-1+0.33.0/MANIFEST.txt @@ -0,0 +1,17 @@ +## Invoked from: /data/cephfs-1/work/projects/cubi-varfish-data/2023-06-05_varfish-db-downloader/varfish-db-downloader/output/full/annonars/alphamissense-grch38-1+0.33.0 +## $ hashdeep -l -r . +## +%%%% HASHDEEP-1.0 +1640,80f643a660de95d39eff874048bd1422,b264309b0e16c816fd2c7968b6d1bfd6996b76fa7d59be997d1f6733152b0c63,./rocksdb/000032.sst +16,1499571836189b80bb3138a553dbd79a,306d61aa07213eb5ff589100ad05aedf9b844bccec89d638b94259494e54d751,./rocksdb/CURRENT 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a/tests/server/annonars/dbsnp-grch37-b151+0.39.0/spec.yaml b/tests/server/annonars/dbsnp-grch37-b151+0.39.0/spec.yaml new file mode 100644 index 00000000..83a7d9c7 --- /dev/null +++ b/tests/server/annonars/dbsnp-grch37-b151+0.39.0/spec.yaml @@ -0,0 +1,18 @@ +dc.identifier: annonars/seqvars/dbsnp:b151+0.39.0-grch37 +dc.title: annonars dbSNP RocksDB Database +dc.creator: NCBI dbSNP Team +dc.contributor: + - VarFish Developer Teams +dc.format: application/x-rocksdb +dc.date: 20240711 +x-version: b151+0.39.0 +x-genome-release: grch37 +dc.description: | + RocksDB built from dbSNP b151 VCF file using the annonars package + v0.39.0 in varfish-downloader v0.3.1.dev53+g2697370. +dc.source: + - PMID:10592272 + - https://www.ncbi.nlm.nih.gov/snp/ +x-created-from: + - name: dbSNP + version: b151 diff --git a/tests/server/annonars/dbsnp-grch38-b151+0.39.0/rocksdb/000010.sst b/tests/server/annonars/dbsnp-grch38-b151+0.39.0/rocksdb/000010.sst new file mode 100644 index 00000000..3014e531 --- 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+oid sha256:97fa7f903e34e992ac7eb7ed9cf43030fa91338b333855144ab117e625968440 +size 80908 diff --git a/tests/server/annonars/dbsnp-grch38-b151+0.39.0/rocksdb/MANIFEST-000005 b/tests/server/annonars/dbsnp-grch38-b151+0.39.0/rocksdb/MANIFEST-000005 new file mode 100644 index 00000000..af950c1b --- /dev/null +++ b/tests/server/annonars/dbsnp-grch38-b151+0.39.0/rocksdb/MANIFEST-000005 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b1166d1f9f414f106d78302ec204c3a1a55a67c19575540ab01a8ad1ca6fef61 +size 766 diff --git a/tests/server/annonars/dbsnp-grch38-b151+0.39.0/rocksdb/OPTIONS-000007 b/tests/server/annonars/dbsnp-grch38-b151+0.39.0/rocksdb/OPTIONS-000007 new file mode 100644 index 00000000..d02a5dae --- /dev/null +++ b/tests/server/annonars/dbsnp-grch38-b151+0.39.0/rocksdb/OPTIONS-000007 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:32bffc8701f20c40a2f9d7b4b5d002fe868473b37467e3564200f52d2b814579 +size 20868 diff --git a/tests/server/annonars/dbsnp-grch38-b151+0.39.0/spec.yaml b/tests/server/annonars/dbsnp-grch38-b151+0.39.0/spec.yaml new file mode 100644 index 00000000..4b28188a --- /dev/null +++ b/tests/server/annonars/dbsnp-grch38-b151+0.39.0/spec.yaml @@ -0,0 +1,18 @@ +dc.identifier: annonars/seqvars/dbsnp:b151+0.39.0-grch38 +dc.title: annonars dbSNP RocksDB Database +dc.creator: NCBI dbSNP Team +dc.contributor: + - VarFish Developer Teams +dc.format: application/x-rocksdb +dc.date: 20240711 +x-version: b151+0.39.0 +x-genome-release: grch38 +dc.description: | + RocksDB built from dbSNP b151 VCF file using the annonars package + v0.39.0 in varfish-downloader v0.3.1.dev53+g2697370. +dc.source: + - PMID:10592272 + - https://www.ncbi.nlm.nih.gov/snp/ +x-created-from: + - name: dbSNP + version: b151 diff --git a/tests/server/annonars/functional-grch37-105.20201022+0.33.0/MANIFEST.txt b/tests/server/annonars/functional-grch37-105.20201022+0.33.0/MANIFEST.txt new file mode 100644 index 00000000..fd1ced3b --- /dev/null +++ b/tests/server/annonars/functional-grch37-105.20201022+0.33.0/MANIFEST.txt @@ -0,0 +1,18 @@ +## Invoked from: /data/cephfs-1/work/projects/cubi-varfish-data/2023-06-05_varfish-db-downloader/varfish-db-downloader/output/full/annonars/functional-grch37-105.20201022+0.33.0 +## $ hashdeep -l -r . +## +%%%% HASHDEEP-1.0 +1342,aa333ecd72063683222b0339e81afae6,17f2a7b6fdd91db1cadd9b7ba29c6776863a9cbc5aed5afe1c5f0cb84a1d8fc7,./rocksdb/000036.sst +345164,7f20e29b6df8d9ef06bf9bfd69b0ce4a,a9c3f7716c6a3c18ba5185bd7eaa9546d11d4b841e7b9b745fc3f3b1d5b01695,./rocksdb/000038.sst +16,6448975c42add63245f521ace330206a,501c24889835a42fd2d2fb53dd035809a93ef24302f84936db3099434eb9d5ae,./rocksdb/CURRENT +36,6c9d028bb745cc98e58bbe05a4d559cb,0c82a9cd51ae7684ee558e00e41d6ad7562d8c5fbe2aaab6be61d0f2ad1760d2,./rocksdb/IDENTITY +0,d41d8cd98f00b204e9800998ecf8427e,e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855,./rocksdb/LOCK +67225,82b3467a16912d3cefbf93f940d045fe,3bc7a5c1d78470989609eb8d3d4f50517e5e83c3976d39258edaaf8944f51676,./rocksdb/LOG +65734,2fdf367f308945c38507b9c1bb8e79f4,eca945a86d52487d0a3ea6c6c1b22451c762f8fca70633da1c840f789649fb63,./rocksdb/LOG.old.1704452291152702 +67224,2aefab576e6407661adfb40b60e7c065,78e10e6bfa21c24bd7c543e58a9a7b64b3fa2aaf058c3b5ce2cfe993d874d828,./rocksdb/LOG.old.1704453750921185 +982,a89337848bd8f1123cb71e249a3aa720,2ea393c47fb851930804d72cec5de75d839d89c69a5f1edee4422441d8fc5753,./rocksdb/MANIFEST-000031 +15363,8b896b1ecb2bc26b05bc0535769af552,8b06754bc4e8868b270619cabf6ed94d2d66e93a527c64059537322bd7414782,./rocksdb/OPTIONS-000022 +15363,8b896b1ecb2bc26b05bc0535769af552,8b06754bc4e8868b270619cabf6ed94d2d66e93a527c64059537322bd7414782,./rocksdb/OPTIONS-000033 +492,3c44563b48e8d1063e1f02f2c0586c0c,56610053537cc3c2ca3a0ff568d8390d7d11efa1fb4be2006b3255b03097da3f,./spec.yaml +%%%% size,md5,sha256,filename +## EOF SHA256=eeba03b0580a41a7f462f2261b4beada0d09cf65304c21bfb9bcbb098b45f75c diff --git a/tests/server/annonars/functional-grch37-105.20201022+0.33.0/rocksdb/000036.sst b/tests/server/annonars/functional-grch37-105.20201022+0.33.0/rocksdb/000036.sst new file mode 100644 index 00000000..fa91ba97 --- /dev/null +++ b/tests/server/annonars/functional-grch37-105.20201022+0.33.0/rocksdb/000036.sst @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:17f2a7b6fdd91db1cadd9b7ba29c6776863a9cbc5aed5afe1c5f0cb84a1d8fc7 +size 1342 diff --git a/tests/server/annonars/functional-grch37-105.20201022+0.33.0/rocksdb/000038.sst b/tests/server/annonars/functional-grch37-105.20201022+0.33.0/rocksdb/000038.sst new file mode 100644 index 00000000..70607d35 --- /dev/null +++ b/tests/server/annonars/functional-grch37-105.20201022+0.33.0/rocksdb/000038.sst @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a9c3f7716c6a3c18ba5185bd7eaa9546d11d4b841e7b9b745fc3f3b1d5b01695 +size 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a/tests/server/annonars/functional-grch37-105.20201022+0.33.0/rocksdb/LOCK b/tests/server/annonars/functional-grch37-105.20201022+0.33.0/rocksdb/LOCK new file mode 100644 index 00000000..e69de29b diff --git a/tests/server/annonars/functional-grch37-105.20201022+0.33.0/rocksdb/LOG b/tests/server/annonars/functional-grch37-105.20201022+0.33.0/rocksdb/LOG new file mode 100644 index 00000000..6481ec8d --- /dev/null +++ b/tests/server/annonars/functional-grch37-105.20201022+0.33.0/rocksdb/LOG @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:3bc7a5c1d78470989609eb8d3d4f50517e5e83c3976d39258edaaf8944f51676 +size 67225 diff --git a/tests/server/annonars/functional-grch37-105.20201022+0.33.0/rocksdb/LOG.old.1704452291152702 b/tests/server/annonars/functional-grch37-105.20201022+0.33.0/rocksdb/LOG.old.1704452291152702 new file mode 100644 index 00000000..47286baa --- /dev/null +++ b/tests/server/annonars/functional-grch37-105.20201022+0.33.0/rocksdb/LOG.old.1704452291152702 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:eca945a86d52487d0a3ea6c6c1b22451c762f8fca70633da1c840f789649fb63 +size 65734 diff --git a/tests/server/annonars/functional-grch37-105.20201022+0.33.0/rocksdb/LOG.old.1704453750921185 b/tests/server/annonars/functional-grch37-105.20201022+0.33.0/rocksdb/LOG.old.1704453750921185 new file mode 100644 index 00000000..38c650bb --- /dev/null +++ b/tests/server/annonars/functional-grch37-105.20201022+0.33.0/rocksdb/LOG.old.1704453750921185 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:78e10e6bfa21c24bd7c543e58a9a7b64b3fa2aaf058c3b5ce2cfe993d874d828 +size 67224 diff --git a/tests/server/annonars/functional-grch37-105.20201022+0.33.0/rocksdb/MANIFEST-000031 b/tests/server/annonars/functional-grch37-105.20201022+0.33.0/rocksdb/MANIFEST-000031 new file mode 100644 index 00000000..d29e94e6 --- /dev/null +++ b/tests/server/annonars/functional-grch37-105.20201022+0.33.0/rocksdb/MANIFEST-000031 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2ea393c47fb851930804d72cec5de75d839d89c69a5f1edee4422441d8fc5753 +size 982 diff --git a/tests/server/annonars/functional-grch37-105.20201022+0.33.0/rocksdb/OPTIONS-000022 b/tests/server/annonars/functional-grch37-105.20201022+0.33.0/rocksdb/OPTIONS-000022 new file mode 100644 index 00000000..dcc7a077 --- /dev/null +++ b/tests/server/annonars/functional-grch37-105.20201022+0.33.0/rocksdb/OPTIONS-000022 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8b06754bc4e8868b270619cabf6ed94d2d66e93a527c64059537322bd7414782 +size 15363 diff --git a/tests/server/annonars/functional-grch37-105.20201022+0.33.0/rocksdb/OPTIONS-000033 b/tests/server/annonars/functional-grch37-105.20201022+0.33.0/rocksdb/OPTIONS-000033 new file mode 100644 index 00000000..dcc7a077 --- /dev/null +++ b/tests/server/annonars/functional-grch37-105.20201022+0.33.0/rocksdb/OPTIONS-000033 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8b06754bc4e8868b270619cabf6ed94d2d66e93a527c64059537322bd7414782 +size 15363 diff --git a/tests/server/annonars/functional-grch37-105.20201022+0.33.0/spec.yaml b/tests/server/annonars/functional-grch37-105.20201022+0.33.0/spec.yaml new file mode 100644 index 00000000..706b3742 --- /dev/null +++ b/tests/server/annonars/functional-grch37-105.20201022+0.33.0/spec.yaml @@ -0,0 +1,16 @@ +dc.identifier: annonars/functional:105.20201022+0.33.0- +dc.title: annonars functional elements RocksDB +dc.creator: VarFish Developer Teams +dc.format: application/x-rocksdb +dc.date: 20240105 +x-version: 105.20201022+0.33.0 +x-genome-release: +dc.description: | + RocksDB built from RefSeq Functional Elements (and other sources in + the future). +dc.source: + - PMID:34876495 + - https://www.ncbi.nlm.nih.gov/refseq/ +x-created-from: + - name: RefSeq Functional Elements + version: 105.20201022 diff --git a/tests/server/annonars/functional-grch38-110+0.33.0/MANIFEST.txt b/tests/server/annonars/functional-grch38-110+0.33.0/MANIFEST.txt new file mode 100644 index 00000000..0822b7c1 --- /dev/null +++ b/tests/server/annonars/functional-grch38-110+0.33.0/MANIFEST.txt @@ -0,0 +1,18 @@ +## Invoked from: /data/cephfs-1/work/projects/cubi-varfish-data/2023-06-05_varfish-db-downloader/varfish-db-downloader/output/full/annonars/functional-grch38-110+0.33.0 +## $ hashdeep -l -r . +## +%%%% HASHDEEP-1.0 +1343,539abccece5b2a015e4ea9494dbbb730,0ad7c22e6136e487af6d6ae0d8fd26fdaa3f44c374a96b04130503f7dc7a1792,./rocksdb/000036.sst +503774,11e84c80d59e6d178c95884fc1c7c3a7,f5f39a7313ee2cafb08b0f15f3f546e0ccd4c7281998cfd11ea34f215871859d,./rocksdb/000038.sst +16,6448975c42add63245f521ace330206a,501c24889835a42fd2d2fb53dd035809a93ef24302f84936db3099434eb9d5ae,./rocksdb/CURRENT +36,b180f240207c8f7ca5d2ba108f1c0cf2,c732e81be62427bb0c6e052fae42daaba9f50e6b0edc7f50153d820347a8fcb3,./rocksdb/IDENTITY +0,d41d8cd98f00b204e9800998ecf8427e,e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855,./rocksdb/LOCK +67148,f652309804d35cbad054b043917e4846,73b2cf032252410f0030cc78e9f21a7f6b8b4f07f4faa9ba2e5431ed46f9b53c,./rocksdb/LOG +65675,79efc10ce1cfc437a48d3f90186ef8d5,f35d248adb4e61967f49af98f901c0759ad38af9717903f217585929c92a14b8,./rocksdb/LOG.old.1704452302780487 +67147,69d99a5ef1266bc22817199323def320,3b822e6df6995b9b10dc77875c6be1d8f97ee3b5f97f07198732ce63c4299f4a,./rocksdb/LOG.old.1704453756670050 +982,398f1c942b77db45f836242b3167ca1c,446fd23d3d2752dab4d69f413120daee6903d27c383f0f75f5813fcd50761f7b,./rocksdb/MANIFEST-000031 +15363,8b896b1ecb2bc26b05bc0535769af552,8b06754bc4e8868b270619cabf6ed94d2d66e93a527c64059537322bd7414782,./rocksdb/OPTIONS-000022 +15363,8b896b1ecb2bc26b05bc0535769af552,8b06754bc4e8868b270619cabf6ed94d2d66e93a527c64059537322bd7414782,./rocksdb/OPTIONS-000033 +465,33f932a76b08f2e60c7d48e7857d3938,a3c23e9e37b3a8a4ee4e689bf06334bd1feebf43fca7a5abb67a5b2115d0d26b,./spec.yaml +%%%% size,md5,sha256,filename +## EOF SHA256=3beaf8e9c6e675aef322b74c4bd351ee436f2490598ffabfff334faa54b7ab80 diff --git a/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/000036.sst b/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/000036.sst new file mode 100644 index 00000000..1cf3da4d --- /dev/null +++ b/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/000036.sst @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0ad7c22e6136e487af6d6ae0d8fd26fdaa3f44c374a96b04130503f7dc7a1792 +size 1343 diff --git a/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/000038.sst b/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/000038.sst new file mode 100644 index 00000000..3095d1c8 --- /dev/null +++ b/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/000038.sst @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f5f39a7313ee2cafb08b0f15f3f546e0ccd4c7281998cfd11ea34f215871859d +size 503774 diff --git a/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/CURRENT b/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/CURRENT new file mode 100644 index 00000000..1a87b731 --- /dev/null +++ b/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/CURRENT @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:501c24889835a42fd2d2fb53dd035809a93ef24302f84936db3099434eb9d5ae +size 16 diff --git a/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/IDENTITY b/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/IDENTITY new file mode 100644 index 00000000..0ba6b4ed --- /dev/null +++ b/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/IDENTITY @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c732e81be62427bb0c6e052fae42daaba9f50e6b0edc7f50153d820347a8fcb3 +size 36 diff --git a/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/LOCK b/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/LOCK new file mode 100644 index 00000000..e69de29b diff --git a/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/LOG b/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/LOG new file mode 100644 index 00000000..cbfeb3e5 --- /dev/null +++ b/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/LOG @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:73b2cf032252410f0030cc78e9f21a7f6b8b4f07f4faa9ba2e5431ed46f9b53c +size 67148 diff --git a/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/LOG.old.1704452302780487 b/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/LOG.old.1704452302780487 new file mode 100644 index 00000000..3a4b8779 --- /dev/null +++ b/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/LOG.old.1704452302780487 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f35d248adb4e61967f49af98f901c0759ad38af9717903f217585929c92a14b8 +size 65675 diff --git a/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/LOG.old.1704453756670050 b/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/LOG.old.1704453756670050 new file mode 100644 index 00000000..1764f290 --- /dev/null +++ b/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/LOG.old.1704453756670050 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:3b822e6df6995b9b10dc77875c6be1d8f97ee3b5f97f07198732ce63c4299f4a +size 67147 diff --git a/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/MANIFEST-000031 b/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/MANIFEST-000031 new file mode 100644 index 00000000..f1a53338 --- /dev/null +++ b/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/MANIFEST-000031 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:446fd23d3d2752dab4d69f413120daee6903d27c383f0f75f5813fcd50761f7b +size 982 diff --git a/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/OPTIONS-000022 b/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/OPTIONS-000022 new file mode 100644 index 00000000..dcc7a077 --- /dev/null +++ b/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/OPTIONS-000022 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8b06754bc4e8868b270619cabf6ed94d2d66e93a527c64059537322bd7414782 +size 15363 diff --git a/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/OPTIONS-000033 b/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/OPTIONS-000033 new file mode 100644 index 00000000..dcc7a077 --- /dev/null +++ b/tests/server/annonars/functional-grch38-110+0.33.0/rocksdb/OPTIONS-000033 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8b06754bc4e8868b270619cabf6ed94d2d66e93a527c64059537322bd7414782 +size 15363 diff --git a/tests/server/annonars/functional-grch38-110+0.33.0/spec.yaml b/tests/server/annonars/functional-grch38-110+0.33.0/spec.yaml new file mode 100644 index 00000000..3f677c30 --- /dev/null +++ b/tests/server/annonars/functional-grch38-110+0.33.0/spec.yaml @@ -0,0 +1,16 @@ +dc.identifier: annonars/functional:110+0.33.0- +dc.title: annonars functional elements RocksDB +dc.creator: VarFish Developer Teams +dc.format: application/x-rocksdb +dc.date: 20240105 +x-version: 110+0.33.0 +x-genome-release: +dc.description: | + RocksDB built from RefSeq Functional Elements (and other sources in + the future). +dc.source: + - PMID:34876495 + - https://www.ncbi.nlm.nih.gov/refseq/ +x-created-from: + - name: RefSeq Functional Elements + version: 110 diff --git a/tests/server/annonars/genes-3.1+4.0+4.5+20230606+10.1+20240105+0.33.0/MANIFEST.txt b/tests/server/annonars/genes-3.1+4.0+4.5+20230606+10.1+20240105+0.33.0/MANIFEST.txt new file mode 100644 index 00000000..c4655c28 --- /dev/null +++ b/tests/server/annonars/genes-3.1+4.0+4.5+20230606+10.1+20240105+0.33.0/MANIFEST.txt @@ -0,0 +1,16 @@ +## Invoked from: /data/cephfs-1/work/projects/cubi-varfish-data/2023-06-05_varfish-db-downloader/varfish-db-downloader/output/full/annonars/genes-3.1+4.0+4.5+20230606+10.1+20240105+0.33.0 +## $ hashdeep -l -r . +## +%%%% HASHDEEP-1.0 +1285,b1ae4fa6c1da8add086b717200a366c9,8d5c273c8ec32c2dbabaeaae97716536346d0dcdc942a027b227160e95a5af9d,./rocksdb/000014.sst +167892339,f871db802c6264c53f50803960d16780,1892313df3173f6c551267aee2965470dd3c177006896a797fd40a1cfa414928,./rocksdb/000016.sst +16,9f36605efba98dab15728fe8b5538aa0,9c283f6e81028b9eb0760d918ee4bc0aa256ed3b926393c1734c760c4bd724fd,./rocksdb/CURRENT +36,1f4f639c228ac157174666e2662cecd5,be4ff5d82883be8635714de4027cae53141360716bee81a78101b4b5c8e6632b,./rocksdb/IDENTITY +0,d41d8cd98f00b204e9800998ecf8427e,e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855,./rocksdb/LOCK +65741,d46af41a2f0a3c7a659c1add3478577a,7b66a13943a474b004343634944cafe14ce560c992e8caf7bff42a191d03e3b1,./rocksdb/LOG +667,561a010291af3919fda7e3825f098314,22da156ec0e2e691805f7ef7a6eed0b5ed4b749a628c043e545adf3a283fade8,./rocksdb/MANIFEST-000005 +15353,6e92121f3f088ca0bdb379c4f6512f42,95c0642e3547609c82800a896eb8f634abeea27cf7175c4b0d1e09c4f3519f2d,./rocksdb/OPTIONS-000009 +15353,6e92121f3f088ca0bdb379c4f6512f42,95c0642e3547609c82800a896eb8f634abeea27cf7175c4b0d1e09c4f3519f2d,./rocksdb/OPTIONS-000011 +1339,3bc19941f8b16530496e13f1353c123b,b49e40493255511195ba30e92414e230e19e47cb75bb25bcab0d4716e3bfa81a,./spec.yaml +%%%% size,md5,sha256,filename +## EOF SHA256=49fd6e378a6fcde5b0d4abdc2f6c434808c9d165cba07aad837e28bbc4a231f8 diff --git a/tests/server/annonars/genes-3.1+4.0+4.5+20230606+10.1+20240105+0.33.0/rocksdb/000014.sst b/tests/server/annonars/genes-3.1+4.0+4.5+20230606+10.1+20240105+0.33.0/rocksdb/000014.sst new file mode 100644 index 00000000..e8ff0b99 --- /dev/null +++ b/tests/server/annonars/genes-3.1+4.0+4.5+20230606+10.1+20240105+0.33.0/rocksdb/000014.sst @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8d5c273c8ec32c2dbabaeaae97716536346d0dcdc942a027b227160e95a5af9d +size 1285 diff --git a/tests/server/annonars/genes-3.1+4.0+4.5+20230606+10.1+20240105+0.33.0/rocksdb/000016.sst b/tests/server/annonars/genes-3.1+4.0+4.5+20230606+10.1+20240105+0.33.0/rocksdb/000016.sst new file mode 100644 index 00000000..d475f61e --- /dev/null +++ b/tests/server/annonars/genes-3.1+4.0+4.5+20230606+10.1+20240105+0.33.0/rocksdb/000016.sst @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:1892313df3173f6c551267aee2965470dd3c177006896a797fd40a1cfa414928 +size 167892339 diff --git a/tests/server/annonars/genes-3.1+4.0+4.5+20230606+10.1+20240105+0.33.0/rocksdb/CURRENT 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b/tests/server/annonars/gnomad-genomes-grch38-4.1+0.39.0/rocksdb/000010.sst new file mode 100644 index 00000000..4c3079d6 --- /dev/null +++ b/tests/server/annonars/gnomad-genomes-grch38-4.1+0.39.0/rocksdb/000010.sst @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4cc02236d9f4d86cb12a573828e8ec0f5d503631630133c4133931cf7beced48 +size 1563 diff --git a/tests/server/annonars/gnomad-genomes-grch38-4.1+0.39.0/rocksdb/000012.sst b/tests/server/annonars/gnomad-genomes-grch38-4.1+0.39.0/rocksdb/000012.sst new file mode 100644 index 00000000..c480f66c --- /dev/null +++ b/tests/server/annonars/gnomad-genomes-grch38-4.1+0.39.0/rocksdb/000012.sst @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:01d9d9a1ccb5cf71e6419f43a38f6307f882201459a2a26060fd354afa74579e +size 60021468 diff --git a/tests/server/annonars/gnomad-genomes-grch38-4.1+0.39.0/rocksdb/CURRENT b/tests/server/annonars/gnomad-genomes-grch38-4.1+0.39.0/rocksdb/CURRENT new file mode 100644 index 00000000..f8d50486 --- /dev/null +++ b/tests/server/annonars/gnomad-genomes-grch38-4.1+0.39.0/rocksdb/CURRENT @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:9c283f6e81028b9eb0760d918ee4bc0aa256ed3b926393c1734c760c4bd724fd +size 16 diff --git a/tests/server/annonars/gnomad-genomes-grch38-4.1+0.39.0/rocksdb/IDENTITY b/tests/server/annonars/gnomad-genomes-grch38-4.1+0.39.0/rocksdb/IDENTITY new file mode 100644 index 00000000..7822d530 --- /dev/null +++ b/tests/server/annonars/gnomad-genomes-grch38-4.1+0.39.0/rocksdb/IDENTITY @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:68d051027c2674cf237c7abae5fb7947b780fa2456490d923ebeb46e8966e607 +size 36 diff --git a/tests/server/annonars/gnomad-genomes-grch38-4.1+0.39.0/rocksdb/LOCK b/tests/server/annonars/gnomad-genomes-grch38-4.1+0.39.0/rocksdb/LOCK new file mode 100644 index 00000000..e69de29b diff --git a/tests/server/annonars/gnomad-genomes-grch38-4.1+0.39.0/rocksdb/LOG b/tests/server/annonars/gnomad-genomes-grch38-4.1+0.39.0/rocksdb/LOG new file mode 100644 index 00000000..e92664e8 --- /dev/null +++ b/tests/server/annonars/gnomad-genomes-grch38-4.1+0.39.0/rocksdb/LOG @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:31f29d622e25dae7df5647a7f13d6abf4f0edbbd85312765e4781bd0b8af639c +size 67818 diff --git a/tests/server/annonars/gnomad-genomes-grch38-4.1+0.39.0/rocksdb/MANIFEST-000005 b/tests/server/annonars/gnomad-genomes-grch38-4.1+0.39.0/rocksdb/MANIFEST-000005 new file mode 100644 index 00000000..d1e39aee --- /dev/null +++ b/tests/server/annonars/gnomad-genomes-grch38-4.1+0.39.0/rocksdb/MANIFEST-000005 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:815bf79dc93c384f9253464365b1d01cb877525c56a5161c5414a19f2fd9eecc +size 735 diff --git a/tests/server/annonars/gnomad-genomes-grch38-4.1+0.39.0/rocksdb/OPTIONS-000007 b/tests/server/annonars/gnomad-genomes-grch38-4.1+0.39.0/rocksdb/OPTIONS-000007 new file mode 100644 index 00000000..5fcafc97 --- /dev/null +++ b/tests/server/annonars/gnomad-genomes-grch38-4.1+0.39.0/rocksdb/OPTIONS-000007 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:906303d98fa07b8bafe4ae137a33f1cb62eb278b729c036271cf2061d4cf3727 +size 16342 diff --git a/tests/server/annonars/gnomad-genomes-grch38-4.1+0.39.0/spec.yaml b/tests/server/annonars/gnomad-genomes-grch38-4.1+0.39.0/spec.yaml new file mode 100644 index 00000000..20d3f3f7 --- /dev/null +++ b/tests/server/annonars/gnomad-genomes-grch38-4.1+0.39.0/spec.yaml @@ -0,0 +1,18 @@ +dc.identifier: annonars/seqvars/gnomad-genomes:4.1+0.39.0-grch38 +dc.title: annonars gnomAD-genomes RocksDB Database +dc.creator: gnomAD Team +dc.contributor: + - VarFish Developer Teams +dc.format: application/x-rocksdb +dc.date: 20240711 +x-version: 4.1+0.39.0 +x-genome-release: grch38 +dc.description: | + RocksDB with the information from gnomAD genomes v4.1 converted with + annonars v0.39.0 in varfish-downloader v0.3.1.dev53+g2697370. +dc.source: + - PMID:32461654 + - https://gnomad.broadinstitute.org/ +x-created-from: + - name: gnomAD-genomes + version: 4.1 diff --git a/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/MANIFEST.txt b/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/MANIFEST.txt new file mode 100644 index 00000000..dacd8513 --- /dev/null +++ b/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/MANIFEST.txt @@ -0,0 +1,18 @@ +## Invoked from: /data/cephfs-1/work/projects/cubi-varfish-data/2023-06-05_varfish-db-downloader/varfish-db-downloader/output/full/annonars/gnomad-mtdna-grch37-3.1+0.33.0 +## $ hashdeep -l -r . +## +%%%% HASHDEEP-1.0 +1325,21f65849f32915fa5ed4afb766c56821,854e8ecb586c2edc1ffca99acaf54520394d548e9e5eca20c352e4ee0b6b74c5,./rocksdb/000036.sst +959974,eea794aba2fb139a26b72bb54dfb6ea1,fbca657a1cafd79609c88841ab1dcf6d3abbf77214012b374620e4dc97056a71,./rocksdb/000038.sst +16,6448975c42add63245f521ace330206a,501c24889835a42fd2d2fb53dd035809a93ef24302f84936db3099434eb9d5ae,./rocksdb/CURRENT +36,486155220c33ed511d4f398cd2e29db3,aaee536183b75b1c64a7319c6713050f567f03dac7bdbf2fca967eec17ae6bb4,./rocksdb/IDENTITY +0,d41d8cd98f00b204e9800998ecf8427e,e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855,./rocksdb/LOCK +67346,d3ff9d0904c3e76436a1e65a873e8d5a,2862bb87459ef405c0f0fcacea2b59def6bfee82651ce6bf8ba63090cb228fd1,./rocksdb/LOG +65868,a87097897d38f06dd2981e260e80c4ae,e21f2bab41aa2660bd3f020c23f7e469568c7663d073f19a81b4686050aa7100,./rocksdb/LOG.old.1704452447447160 +67345,f18b4e7aaf34e12f481addf13910da3e,4524571af210f9d4a26d584d0b2124cd73d095f3ab19a185434821ea2e0b98a2,./rocksdb/LOG.old.1704453770381682 +924,500cb4378f09c05ac17a2321a6167534,7a3b1fd5245b05999c5b4eeab11cd63090404fc015fad1f9f9d7834f48f72eef,./rocksdb/MANIFEST-000031 +15377,7b7f3af36e60fc4c73a06bab3593eb06,45a64af152b159348e1c69942f31af102cb0a3fe1905537a4bd95f83d41fb3d4,./rocksdb/OPTIONS-000022 +15377,7b7f3af36e60fc4c73a06bab3593eb06,45a64af152b159348e1c69942f31af102cb0a3fe1905537a4bd95f83d41fb3d4,./rocksdb/OPTIONS-000033 +563,8518aea44c2c558f2e183de34ad03c02,8dc5cdc971e0d437cad6c3d7d1a224894358f40c70f5e997d90c99c4ffe811b1,./spec.yaml +%%%% size,md5,sha256,filename +## EOF SHA256=cc99ac09de88f6f3eb1caca930d8e0028d432148c0c19f75d251f989ddf55c0a diff --git a/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/000036.sst b/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/000036.sst new file mode 100644 index 00000000..265151d3 --- /dev/null +++ b/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/000036.sst @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:854e8ecb586c2edc1ffca99acaf54520394d548e9e5eca20c352e4ee0b6b74c5 +size 1325 diff --git a/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/000038.sst b/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/000038.sst new file mode 100644 index 00000000..6ebd5fab --- /dev/null +++ b/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/000038.sst @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:fbca657a1cafd79609c88841ab1dcf6d3abbf77214012b374620e4dc97056a71 +size 959974 diff --git a/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/CURRENT b/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/CURRENT new file mode 100644 index 00000000..1a87b731 --- /dev/null +++ b/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/CURRENT @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:501c24889835a42fd2d2fb53dd035809a93ef24302f84936db3099434eb9d5ae +size 16 diff --git a/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/IDENTITY b/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/IDENTITY new file mode 100644 index 00000000..b28dcaff --- /dev/null +++ b/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/IDENTITY @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:aaee536183b75b1c64a7319c6713050f567f03dac7bdbf2fca967eec17ae6bb4 +size 36 diff --git a/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/LOCK b/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/LOCK new file mode 100644 index 00000000..e69de29b diff --git a/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/LOG b/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/LOG new file mode 100644 index 00000000..13a46d7e --- /dev/null +++ b/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/LOG @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2862bb87459ef405c0f0fcacea2b59def6bfee82651ce6bf8ba63090cb228fd1 +size 67346 diff --git a/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/LOG.old.1704452447447160 b/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/LOG.old.1704452447447160 new file mode 100644 index 00000000..e5758559 --- /dev/null +++ b/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/LOG.old.1704452447447160 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e21f2bab41aa2660bd3f020c23f7e469568c7663d073f19a81b4686050aa7100 +size 65868 diff --git a/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/LOG.old.1704453770381682 b/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/LOG.old.1704453770381682 new file mode 100644 index 00000000..b47ab14c --- /dev/null +++ b/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/LOG.old.1704453770381682 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4524571af210f9d4a26d584d0b2124cd73d095f3ab19a185434821ea2e0b98a2 +size 67345 diff --git a/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/MANIFEST-000031 b/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/MANIFEST-000031 new file mode 100644 index 00000000..4193ee89 --- /dev/null +++ b/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/MANIFEST-000031 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:7a3b1fd5245b05999c5b4eeab11cd63090404fc015fad1f9f9d7834f48f72eef +size 924 diff --git a/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/OPTIONS-000022 b/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/OPTIONS-000022 new file mode 100644 index 00000000..516bdeac --- /dev/null +++ b/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/OPTIONS-000022 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:45a64af152b159348e1c69942f31af102cb0a3fe1905537a4bd95f83d41fb3d4 +size 15377 diff --git a/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/OPTIONS-000033 b/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/OPTIONS-000033 new file mode 100644 index 00000000..516bdeac --- /dev/null +++ b/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/rocksdb/OPTIONS-000033 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:45a64af152b159348e1c69942f31af102cb0a3fe1905537a4bd95f83d41fb3d4 +size 15377 diff --git a/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/spec.yaml b/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/spec.yaml new file mode 100644 index 00000000..2696f710 --- /dev/null +++ b/tests/server/annonars/gnomad-mtdna-grch37-3.1+0.33.0/spec.yaml @@ -0,0 +1,18 @@ +dc.identifier: annonars/seqvars/gnomad-mtdna:3.1+0.33.0-grch37 +dc.title: annonars gnomAD-mtDNA RocksDB Database +dc.creator: gnomAD Team +dc.contributor: + - VarFish Developer Teams +dc.format: application/x-rocksdb +dc.date: 20240105 +x-version: 3.1+0.33.0 +x-genome-release: grch37 +dc.description: | + RocksDB with the information from gnomAD mtDNA v3.1 converted with + annonars v0.33.0 in varfish-downloader v0.3.1.dev42+g3a332a0.d20240105. +dc.source: + - PMID:32461654 + - https://gnomad.broadinstitute.org/ +x-created-from: + - name: gnomAD-mtDNA + version: 3.1 diff --git a/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/MANIFEST.txt b/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/MANIFEST.txt new file mode 100644 index 00000000..0df7dae9 --- /dev/null +++ b/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/MANIFEST.txt @@ -0,0 +1,17 @@ +## Invoked from: /data/cephfs-1/work/projects/cubi-varfish-data/2023-06-05_varfish-db-downloader/varfish-db-downloader/output/full/annonars/gnomad-mtdna-grch38-3.1+0.33.0 +## $ hashdeep -l -r . +## +%%%% HASHDEEP-1.0 +1325,6e66fe758e06c3e3cb499d31440a6c0b,e8100cb51d25287d42302c789dc05f9423913c650e94b8c6daf13c0ea5d5420e,./rocksdb/000025.sst +961424,9ef27b9dacbb1bb7b0fa40cceba077cf,cc2577db765695833e4a3d449aeaacac8c26de569371da066fe712fdc8d76fbb,./rocksdb/000027.sst +16,a874f3e3462932a0c15ed8f780124fc5,01bd196d6a114691ec642082ebf6591765c0168d4098a0cd834869bd11c8b87d,./rocksdb/CURRENT +36,aa3e110a2496a319454e572286ab62fc,18be087e31d4e57057607817db45b1a9d97928f8579d96db412123da07b3887c,./rocksdb/IDENTITY +0,d41d8cd98f00b204e9800998ecf8427e,e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855,./rocksdb/LOCK +67343,ec7397ff0425a6cbb06a62fa2142792d,588ba95a0ae52b9be50d677b5fdf88dbd146e64a87e6554fcba4772e634e5fdd,./rocksdb/LOG +65867,26a7d3c01df9885825e69982e5c23b5a,52348ee86efcfbae14556fbb39f59b9bd82163605bd73c3f04ffff52c52ff27f,./rocksdb/LOG.old.1704453865399269 +924,0cdd013399728e22fbe7c88d1751bdc9,c4a7a213bef83e899efb621799c148ee88a6316da68c0818504af54b6f5ebda4,./rocksdb/MANIFEST-000020 +15377,7b7f3af36e60fc4c73a06bab3593eb06,45a64af152b159348e1c69942f31af102cb0a3fe1905537a4bd95f83d41fb3d4,./rocksdb/OPTIONS-000011 +15377,7b7f3af36e60fc4c73a06bab3593eb06,45a64af152b159348e1c69942f31af102cb0a3fe1905537a4bd95f83d41fb3d4,./rocksdb/OPTIONS-000022 +563,40423b1186751deb463dca9abf51de98,09ad979a8657c4eacc0d3848e5f8b0fc5ae94572b228adbed875804f091b7293,./spec.yaml +%%%% size,md5,sha256,filename +## EOF SHA256=7ce8293dfe7eda6a0b2e62f18f10b13335c7b48117c7d61e036e76109e521bb8 diff --git a/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/rocksdb/000025.sst b/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/rocksdb/000025.sst new file mode 100644 index 00000000..11c64221 --- /dev/null +++ b/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/rocksdb/000025.sst @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e8100cb51d25287d42302c789dc05f9423913c650e94b8c6daf13c0ea5d5420e +size 1325 diff --git a/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/rocksdb/000027.sst b/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/rocksdb/000027.sst new file mode 100644 index 00000000..6b469696 --- /dev/null +++ b/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/rocksdb/000027.sst @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:cc2577db765695833e4a3d449aeaacac8c26de569371da066fe712fdc8d76fbb +size 961424 diff --git a/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/rocksdb/CURRENT b/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/rocksdb/CURRENT new file mode 100644 index 00000000..6e219f29 --- /dev/null +++ b/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/rocksdb/CURRENT @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:01bd196d6a114691ec642082ebf6591765c0168d4098a0cd834869bd11c8b87d +size 16 diff --git a/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/rocksdb/IDENTITY b/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/rocksdb/IDENTITY new file mode 100644 index 00000000..b73980ce --- /dev/null +++ b/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/rocksdb/IDENTITY @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:18be087e31d4e57057607817db45b1a9d97928f8579d96db412123da07b3887c +size 36 diff --git a/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/rocksdb/LOCK b/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/rocksdb/LOCK new file mode 100644 index 00000000..e69de29b diff --git a/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/rocksdb/LOG b/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/rocksdb/LOG new file mode 100644 index 00000000..ceaab2ab --- /dev/null +++ b/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/rocksdb/LOG @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:588ba95a0ae52b9be50d677b5fdf88dbd146e64a87e6554fcba4772e634e5fdd +size 67343 diff --git a/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/rocksdb/LOG.old.1704453865399269 b/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/rocksdb/LOG.old.1704453865399269 new file mode 100644 index 00000000..8bf7f126 --- /dev/null +++ b/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/rocksdb/LOG.old.1704453865399269 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:52348ee86efcfbae14556fbb39f59b9bd82163605bd73c3f04ffff52c52ff27f +size 65867 diff --git a/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/rocksdb/MANIFEST-000020 b/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/rocksdb/MANIFEST-000020 new file mode 100644 index 00000000..1e6e082f --- /dev/null +++ b/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/rocksdb/MANIFEST-000020 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c4a7a213bef83e899efb621799c148ee88a6316da68c0818504af54b6f5ebda4 +size 924 diff --git a/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/rocksdb/OPTIONS-000011 b/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/rocksdb/OPTIONS-000011 new file mode 100644 index 00000000..516bdeac --- /dev/null +++ b/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/rocksdb/OPTIONS-000011 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:45a64af152b159348e1c69942f31af102cb0a3fe1905537a4bd95f83d41fb3d4 +size 15377 diff --git a/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/rocksdb/OPTIONS-000022 b/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/rocksdb/OPTIONS-000022 new file mode 100644 index 00000000..516bdeac --- /dev/null +++ b/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/rocksdb/OPTIONS-000022 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:45a64af152b159348e1c69942f31af102cb0a3fe1905537a4bd95f83d41fb3d4 +size 15377 diff --git a/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/spec.yaml b/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/spec.yaml new file mode 100644 index 00000000..d1fcc5c2 --- /dev/null +++ b/tests/server/annonars/gnomad-mtdna-grch38-3.1+0.33.0/spec.yaml @@ -0,0 +1,18 @@ +dc.identifier: annonars/seqvars/gnomad-mtdna:3.1+0.33.0-grch38 +dc.title: annonars gnomAD-mtDNA RocksDB Database +dc.creator: gnomAD Team +dc.contributor: + - VarFish Developer Teams +dc.format: application/x-rocksdb +dc.date: 20240105 +x-version: 3.1+0.33.0 +x-genome-release: grch38 +dc.description: | + RocksDB with the information from gnomAD mtDNA v3.1 converted with + annonars v0.33.0 in varfish-downloader v0.3.1.dev42+g3a332a0.d20240105. +dc.source: + - PMID:32461654 + - https://gnomad.broadinstitute.org/ +x-created-from: + - name: gnomAD-mtDNA + version: 3.1 diff --git a/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/MANIFEST.txt b/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/MANIFEST.txt new file mode 100644 index 00000000..cb3ea7ea --- /dev/null +++ b/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/MANIFEST.txt @@ -0,0 +1,18 @@ +## Invoked from: /data/cephfs-1/work/projects/cubi-varfish-data/2023-06-05_varfish-db-downloader/varfish-db-downloader/output/full/annonars/helixmtdb-grch37-20200327+0.33.0 +## $ hashdeep -l -r . +## +%%%% HASHDEEP-1.0 +1314,fed74d2c55a7e3f4d20cb75eb4372d98,18c1012f868955532928fc66de8f50efbd9e893413bd8cbf9a2012ce9d8ce7d6,./rocksdb/000036.sst +176384,1dc6094d935886e9538c368e41bc9d34,b59f674ddd55921eeb427a421b6db3c81a0097a17d68faedde81a84598eb49bf,./rocksdb/000038.sst +16,6448975c42add63245f521ace330206a,501c24889835a42fd2d2fb53dd035809a93ef24302f84936db3099434eb9d5ae,./rocksdb/CURRENT +36,1059493cfb1ee99ea10147362d02bf4f,0a38d579524de73f16e652752a00c2c9887314876acd4d05d5d468a5473b5f16,./rocksdb/IDENTITY +0,d41d8cd98f00b204e9800998ecf8427e,e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855,./rocksdb/LOCK +67267,454dc67fdb0232f0c143f2e090291928,b26a009b3b5c3660267abf174dae682584b1fabd6a945358c624c810ef39999c,./rocksdb/LOG +65787,ec41ef624502c79870ddaa1c2b0c370c,154ff19ad1ced8072fa396b123f98e7644006e62fd001b70683e901f9d39cd42,./rocksdb/LOG.old.1704452291081261 +67264,7d7ce0bfc18e182b83a84a594fd1edca,35b6342a8015f2c0315092dafeb8be4945d0d52a97ac5ec54a7a71b7da6cfac6,./rocksdb/LOG.old.1704453746301569 +920,a969f43a2f9f69df85a5c04a138791da,913ae903c0f7d98f07989287c6918769acadf51034df75422834f24c4f240c89,./rocksdb/MANIFEST-000031 +15371,8d163c9bfaadf77b01964cca4b1dc0e7,c855c3e36545e034b32c09c47699fb27a1d821919609e3a513d298bf7196ece3,./rocksdb/OPTIONS-000022 +15371,8d163c9bfaadf77b01964cca4b1dc0e7,c855c3e36545e034b32c09c47699fb27a1d821919609e3a513d298bf7196ece3,./rocksdb/OPTIONS-000033 +595,653d8640a2633176984816ae8be78d57,f7537dd836ea8cfeab82866310b0a7ebd54ae7778e09f9ce1c04e817d78a42ec,./spec.yaml +%%%% size,md5,sha256,filename +## EOF SHA256=86865c8093338bf3be284f2dc174b14196869642ae6c46379140bd30463b7613 diff --git a/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/000036.sst b/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/000036.sst new file mode 100644 index 00000000..bfff65df --- /dev/null +++ b/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/000036.sst @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:18c1012f868955532928fc66de8f50efbd9e893413bd8cbf9a2012ce9d8ce7d6 +size 1314 diff --git a/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/000038.sst b/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/000038.sst new file mode 100644 index 00000000..062f08bb --- /dev/null +++ b/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/000038.sst @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b59f674ddd55921eeb427a421b6db3c81a0097a17d68faedde81a84598eb49bf +size 176384 diff --git a/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/CURRENT b/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/CURRENT new file mode 100644 index 00000000..1a87b731 --- /dev/null +++ b/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/CURRENT @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:501c24889835a42fd2d2fb53dd035809a93ef24302f84936db3099434eb9d5ae +size 16 diff --git a/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/IDENTITY b/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/IDENTITY new file mode 100644 index 00000000..347d3be5 --- /dev/null +++ b/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/IDENTITY @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0a38d579524de73f16e652752a00c2c9887314876acd4d05d5d468a5473b5f16 +size 36 diff --git a/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/LOCK b/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/LOCK new file mode 100644 index 00000000..e69de29b diff --git a/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/LOG b/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/LOG new file mode 100644 index 00000000..3d3113cf --- /dev/null +++ b/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/LOG @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b26a009b3b5c3660267abf174dae682584b1fabd6a945358c624c810ef39999c +size 67267 diff --git a/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/LOG.old.1704452291081261 b/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/LOG.old.1704452291081261 new file mode 100644 index 00000000..5716b143 --- /dev/null +++ b/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/LOG.old.1704452291081261 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:154ff19ad1ced8072fa396b123f98e7644006e62fd001b70683e901f9d39cd42 +size 65787 diff --git a/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/LOG.old.1704453746301569 b/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/LOG.old.1704453746301569 new file mode 100644 index 00000000..193d7fad --- /dev/null +++ b/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/LOG.old.1704453746301569 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:35b6342a8015f2c0315092dafeb8be4945d0d52a97ac5ec54a7a71b7da6cfac6 +size 67264 diff --git a/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/MANIFEST-000031 b/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/MANIFEST-000031 new file mode 100644 index 00000000..aefd153b --- /dev/null +++ b/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/MANIFEST-000031 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:913ae903c0f7d98f07989287c6918769acadf51034df75422834f24c4f240c89 +size 920 diff --git a/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/OPTIONS-000022 b/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/OPTIONS-000022 new file mode 100644 index 00000000..1bf8b374 --- /dev/null +++ b/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/OPTIONS-000022 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c855c3e36545e034b32c09c47699fb27a1d821919609e3a513d298bf7196ece3 +size 15371 diff --git a/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/OPTIONS-000033 b/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/OPTIONS-000033 new file mode 100644 index 00000000..1bf8b374 --- /dev/null +++ b/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/rocksdb/OPTIONS-000033 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c855c3e36545e034b32c09c47699fb27a1d821919609e3a513d298bf7196ece3 +size 15371 diff --git a/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/spec.yaml b/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/spec.yaml new file mode 100644 index 00000000..0fde9061 --- /dev/null +++ b/tests/server/annonars/helixmtdb-grch37-20200327+0.33.0/spec.yaml @@ -0,0 +1,18 @@ +dc.identifier: annonars/seqvars/helixmtdb:20200327+0.33.0-grch37 +dc.title: annonars HelixMtDb RocksDB Database +dc.creator: Helix OpCo, LLC +dc.contributor: + - VarFish Developer Teams +dc.format: application/x-rocksdb +dc.date: 20240105 +x-version: 20200327+0.33.0 +x-genome-release: grch37 +dc.description: | + RocksDB with the information from HelixMtDb v20200327 imported using + the annonars package v0.33.0 in varfish-downloader + v0.3.1.dev42+g3a332a0.d20240105. +dc.source: + - https://www.helix.com/pages/mitochondrial-variant-database +x-created-from: + - name: HelixMtdB + version: 20200327 diff --git a/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/MANIFEST.txt b/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/MANIFEST.txt new file mode 100644 index 00000000..16eeda9a --- /dev/null +++ b/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/MANIFEST.txt @@ -0,0 +1,18 @@ +## Invoked from: /data/cephfs-1/work/projects/cubi-varfish-data/2023-06-05_varfish-db-downloader/varfish-db-downloader/output/full/annonars/helixmtdb-grch38-20200327+0.33.0 +## $ hashdeep -l -r . +## +%%%% HASHDEEP-1.0 +1314,4e022419a9f96f54f4381bb993882ed1,68685064f05e8622292b435332527a9b0e4616368d17e6526fe7a6d852af0918,./rocksdb/000036.sst +176384,768e8b28442e622502611b0af23084bf,836b9a9d162bbf4d89ef7c07bb665fd4f038fda44b07b5f007309232f0f38b1f,./rocksdb/000038.sst +16,6448975c42add63245f521ace330206a,501c24889835a42fd2d2fb53dd035809a93ef24302f84936db3099434eb9d5ae,./rocksdb/CURRENT +36,10d72506af28bb0ead905b2c1ce75ec3,6302cd9c39c3737130e8077e539fdeb6417c3c1c031cbc25c3adacdd1fc1c8d8,./rocksdb/IDENTITY +0,d41d8cd98f00b204e9800998ecf8427e,e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855,./rocksdb/LOCK +67263,8a2459a6322ff26c9fda3fd17b68c830,e7ddec9370d935f8dd044566c2522bddc15e8c34d35cba197eb3a968c5c7a291,./rocksdb/LOG +65783,a1899f8e393be3475c810a4501f88160,f7666780d53764a73b85ba2ef2cc8aaedc0c8c27c816bdfeb7057ad01ce76d1d,./rocksdb/LOG.old.1704452313589549 +67266,8def86810b7d0ce6406fb890c2f42e49,39a2b3a790995d3883c757ea3840c4bd1b83c94f5cb9cda15c3c855fc7830366,./rocksdb/LOG.old.1704453751153649 +920,fd00f3d69d7aad4891b2c9a4662654a0,96c216b3cb589a58219a62e6cdd2c56e7476c18227e7604394a1ffe01b7a281b,./rocksdb/MANIFEST-000031 +15371,8d163c9bfaadf77b01964cca4b1dc0e7,c855c3e36545e034b32c09c47699fb27a1d821919609e3a513d298bf7196ece3,./rocksdb/OPTIONS-000022 +15371,8d163c9bfaadf77b01964cca4b1dc0e7,c855c3e36545e034b32c09c47699fb27a1d821919609e3a513d298bf7196ece3,./rocksdb/OPTIONS-000033 +595,8961a7ba73b20805ef70df157a851f80,8abeabb0f534ad653fafb308d93933913a709ada4e011dd4fba48313a7f546ed,./spec.yaml +%%%% size,md5,sha256,filename +## EOF SHA256=286ffdc983ba5395415ccb3b7f9e29c7d9942654148e63945ce94a95cb810aea diff --git a/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/000036.sst b/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/000036.sst new file mode 100644 index 00000000..141d644c --- /dev/null +++ b/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/000036.sst @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:68685064f05e8622292b435332527a9b0e4616368d17e6526fe7a6d852af0918 +size 1314 diff --git a/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/000038.sst b/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/000038.sst new file mode 100644 index 00000000..229bb745 --- /dev/null +++ b/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/000038.sst @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:836b9a9d162bbf4d89ef7c07bb665fd4f038fda44b07b5f007309232f0f38b1f +size 176384 diff --git a/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/CURRENT b/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/CURRENT new file mode 100644 index 00000000..1a87b731 --- /dev/null +++ b/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/CURRENT @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:501c24889835a42fd2d2fb53dd035809a93ef24302f84936db3099434eb9d5ae +size 16 diff --git a/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/IDENTITY b/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/IDENTITY new file mode 100644 index 00000000..93e9a166 --- /dev/null +++ b/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/IDENTITY @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6302cd9c39c3737130e8077e539fdeb6417c3c1c031cbc25c3adacdd1fc1c8d8 +size 36 diff --git a/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/LOCK b/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/LOCK new file mode 100644 index 00000000..e69de29b diff --git a/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/LOG b/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/LOG new file mode 100644 index 00000000..40e714d2 --- /dev/null +++ b/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/LOG @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e7ddec9370d935f8dd044566c2522bddc15e8c34d35cba197eb3a968c5c7a291 +size 67263 diff --git a/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/LOG.old.1704452313589549 b/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/LOG.old.1704452313589549 new file mode 100644 index 00000000..b7407902 --- /dev/null +++ b/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/LOG.old.1704452313589549 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f7666780d53764a73b85ba2ef2cc8aaedc0c8c27c816bdfeb7057ad01ce76d1d +size 65783 diff --git a/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/LOG.old.1704453751153649 b/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/LOG.old.1704453751153649 new file mode 100644 index 00000000..3ab3d65f --- /dev/null +++ b/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/LOG.old.1704453751153649 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:39a2b3a790995d3883c757ea3840c4bd1b83c94f5cb9cda15c3c855fc7830366 +size 67266 diff --git a/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/MANIFEST-000031 b/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/MANIFEST-000031 new file mode 100644 index 00000000..903d4795 --- /dev/null +++ b/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/MANIFEST-000031 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:96c216b3cb589a58219a62e6cdd2c56e7476c18227e7604394a1ffe01b7a281b +size 920 diff --git a/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/OPTIONS-000022 b/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/OPTIONS-000022 new file mode 100644 index 00000000..1bf8b374 --- /dev/null +++ b/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/OPTIONS-000022 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c855c3e36545e034b32c09c47699fb27a1d821919609e3a513d298bf7196ece3 +size 15371 diff --git a/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/OPTIONS-000033 b/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/OPTIONS-000033 new file mode 100644 index 00000000..1bf8b374 --- /dev/null +++ b/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/rocksdb/OPTIONS-000033 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c855c3e36545e034b32c09c47699fb27a1d821919609e3a513d298bf7196ece3 +size 15371 diff --git a/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/spec.yaml b/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/spec.yaml new file mode 100644 index 00000000..9f305815 --- /dev/null +++ b/tests/server/annonars/helixmtdb-grch38-20200327+0.33.0/spec.yaml @@ -0,0 +1,18 @@ +dc.identifier: annonars/seqvars/helixmtdb:20200327+0.33.0-grch38 +dc.title: annonars HelixMtDb RocksDB Database +dc.creator: Helix OpCo, LLC +dc.contributor: + - VarFish Developer Teams +dc.format: application/x-rocksdb +dc.date: 20240105 +x-version: 20200327+0.33.0 +x-genome-release: grch38 +dc.description: | + RocksDB with the information from HelixMtDb v20200327 imported using + the annonars package v0.33.0 in varfish-downloader + v0.3.1.dev42+g3a332a0.d20240105. +dc.source: + - https://www.helix.com/pages/mitochondrial-variant-database +x-created-from: + - name: HelixMtdB + version: 20200327 diff --git a/tests/server/bootstrap.sh b/tests/server/bootstrap.sh new file mode 100644 index 00000000..f16288d3 --- /dev/null +++ b/tests/server/bootstrap.sh @@ -0,0 +1,49 @@ +#!/usr/bin/bash + +# Download annonars file reduced to "for dev" subset. + +SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd ) + +REDUCED_DEV_PATHS=" +cadd-grch37-1.6+0.39.0 +cadd-grch38-1.6+0.39.0 +dbnsfp-grch37-4.5a+0.39.0 +dbnsfp-grch37-4.5c+0.39.0 +dbnsfp-grch38-4.5a+0.39.0 +dbnsfp-grch38-4.5c+0.39.0 +dbsnp-grch37-b151+0.39.0 +dbsnp-grch38-b151+0.39.0 +gnomad-exomes-grch37-2.1.1+0.39.0 +gnomad-exomes-grch38-4.1+0.39.0 +gnomad-genomes-grch37-2.1.1+0.39.0 +gnomad-genomes-grch38-4.1+0.39.0 +" +FULL_PATHS=" +alphamissense-grch37-1+0.33.0 +alphamissense-grch38-1+0.33.0 +functional-grch37-105.20201022+0.33.0 +functional-grch38-110+0.33.0 +genes-3.1+4.0+4.5+20230606+10.1+20240105+0.33.0 +gnomad-mtdna-grch37-3.1+0.33.0 +gnomad-mtdna-grch38-3.1+0.33.0 +helixmtdb-grch37-20200327+0.33.0 +helixmtdb-grch38-20200327+0.33.0 +" + +mkdir -p $SCRIPT_DIR/annonars + +for path in $REDUCED_DEV_PATHS; do + s5cmd \ + --endpoint-url https://ceph-s3-ext.cubi.bihealth.org \ + --no-sign-request \ + sync "s3://varfish-public/reduced-dev/annonars/$path/*" \ + $SCRIPT_DIR/annonars/$path/ +done + +for path in $FULL_PATHS; do + s5cmd \ + --endpoint-url https://ceph-s3-ext.cubi.bihealth.org \ + --no-sign-request \ + sync "s3://varfish-public/full/annonars/$path/*" \ + $SCRIPT_DIR/annonars/$path/ +done