From bb01d4f248f2088c6d51b3896c4ccb7f2ee62b95 Mon Sep 17 00:00:00 2001
From: Benjamin Wingfield <bwingfield@ebi.ac.uk>
Date: Mon, 19 Jun 2023 18:39:12 +0100
Subject: [PATCH] add cli and message validation
---
Cargo.lock | 1029 +++++++++++++++++++++++++++++++++++++++-
Cargo.toml | 5 +
src/main.rs | 83 +++-
src/request/message.rs | 109 +++++
src/request/schema.rs | 4 +-
5 files changed, 1210 insertions(+), 20 deletions(-)
create mode 100644 src/request/message.rs
diff --git a/Cargo.lock b/Cargo.lock
index c2da439..7069ae3 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -2,6 +2,19 @@
# It is not intended for manual editing.
version = 3
+[[package]]
+name = "ahash"
+version = "0.8.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2c99f64d1e06488f620f932677e24bc6e2897582980441ae90a671415bd7ec2f"
+dependencies = [
+ "cfg-if",
+ "getrandom",
+ "once_cell",
+ "serde",
+ "version_check",
+]
+
[[package]]
name = "aho-corasick"
version = "1.0.2"
@@ -11,18 +24,181 @@ dependencies = [
"memchr",
]
+[[package]]
+name = "anstream"
+version = "0.3.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0ca84f3628370c59db74ee214b3263d58f9aadd9b4fe7e711fd87dc452b7f163"
+dependencies = [
+ "anstyle",
+ "anstyle-parse",
+ "anstyle-query",
+ "anstyle-wincon",
+ "colorchoice",
+ "is-terminal",
+ "utf8parse",
+]
+
+[[package]]
+name = "anstyle"
+version = "1.0.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "41ed9a86bf92ae6580e0a31281f65a1b1d867c0cc68d5346e2ae128dddfa6a7d"
+
+[[package]]
+name = "anstyle-parse"
+version = "0.2.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e765fd216e48e067936442276d1d57399e37bce53c264d6fefbe298080cb57ee"
+dependencies = [
+ "utf8parse",
+]
+
+[[package]]
+name = "anstyle-query"
+version = "1.0.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5ca11d4be1bab0c8bc8734a9aa7bf4ee8316d462a08c6ac5052f888fef5b494b"
+dependencies = [
+ "windows-sys",
+]
+
+[[package]]
+name = "anstyle-wincon"
+version = "1.0.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "180abfa45703aebe0093f79badacc01b8fd4ea2e35118747e5811127f926e188"
+dependencies = [
+ "anstyle",
+ "windows-sys",
+]
+
+[[package]]
+name = "anyhow"
+version = "1.0.71"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9c7d0618f0e0b7e8ff11427422b64564d5fb0be1940354bfe2e0529b18a9d9b8"
+
+[[package]]
+name = "autocfg"
+version = "1.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa"
+
+[[package]]
+name = "base64"
+version = "0.21.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "604178f6c5c21f02dc555784810edfb88d34ac2c73b2eae109655649ee73ce3d"
+
+[[package]]
+name = "bit-set"
+version = "0.5.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0700ddab506f33b20a03b13996eccd309a48e5ff77d0d95926aa0210fb4e95f1"
+dependencies = [
+ "bit-vec",
+]
+
+[[package]]
+name = "bit-vec"
+version = "0.6.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "349f9b6a179ed607305526ca489b34ad0a41aed5f7980fa90eb03160b69598fb"
+
[[package]]
name = "bitflags"
version = "1.3.2"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a"
+[[package]]
+name = "bumpalo"
+version = "3.13.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a3e2c3daef883ecc1b5d58c15adae93470a91d425f3532ba1695849656af3fc1"
+
+[[package]]
+name = "bytecount"
+version = "0.6.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2c676a478f63e9fa2dd5368a42f28bba0d6c560b775f38583c8bbaa7fcd67c9c"
+
+[[package]]
+name = "bytes"
+version = "1.4.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "89b2fd2a0dcf38d7971e2194b6b6eebab45ae01067456a7fd93d5547a61b70be"
+
[[package]]
name = "cc"
version = "1.0.79"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "50d30906286121d95be3d479533b458f87493b30a4b5f79a607db8f5d11aa91f"
+[[package]]
+name = "cfg-if"
+version = "1.0.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd"
+
+[[package]]
+name = "clap"
+version = "4.3.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "80672091db20273a15cf9fdd4e47ed43b5091ec9841bf4c6145c9dfbbcae09ed"
+dependencies = [
+ "clap_builder",
+ "clap_derive",
+ "once_cell",
+]
+
+[[package]]
+name = "clap_builder"
+version = "4.3.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c1458a1df40e1e2afebb7ab60ce55c1fa8f431146205aa5f4887e0b111c27636"
+dependencies = [
+ "anstream",
+ "anstyle",
+ "bitflags",
+ "clap_lex",
+ "strsim",
+]
+
+[[package]]
+name = "clap_derive"
+version = "4.3.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b8cd2b2a819ad6eec39e8f1d6b53001af1e5469f8c177579cdaeb313115b825f"
+dependencies = [
+ "heck",
+ "proc-macro2",
+ "quote",
+ "syn",
+]
+
+[[package]]
+name = "clap_lex"
+version = "0.5.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2da6da31387c7e4ef160ffab6d5e7f00c42626fe39aea70a7b0f1773f7dd6c1b"
+
+[[package]]
+name = "colorchoice"
+version = "1.0.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "acbf1af155f9b9ef647e42cdc158db4b64a1b61f743629225fde6f3e0be2a7c7"
+
+[[package]]
+name = "encoding_rs"
+version = "0.8.32"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "071a31f4ee85403370b58aca746f01041ede6f0da2730960ad001edc2b71b394"
+dependencies = [
+ "cfg-if",
+]
+
[[package]]
name = "env_logger"
version = "0.10.0"
@@ -57,13 +233,154 @@ dependencies = [
"libc",
]
+[[package]]
+name = "fancy-regex"
+version = "0.11.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b95f7c0680e4142284cf8b22c14a476e87d61b004a3a0861872b32ef7ead40a2"
+dependencies = [
+ "bit-set",
+ "regex",
+]
+
+[[package]]
+name = "fnv"
+version = "1.0.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3f9eec918d3f24069decb9af1554cad7c880e2da24a9afd88aca000531ab82c1"
+
+[[package]]
+name = "form_urlencoded"
+version = "1.2.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a62bc1cf6f830c2ec14a513a9fb124d0a213a629668a4186f329db21fe045652"
+dependencies = [
+ "percent-encoding",
+]
+
+[[package]]
+name = "fraction"
+version = "0.13.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3027ae1df8d41b4bed2241c8fdad4acc1e7af60c8e17743534b545e77182d678"
+dependencies = [
+ "lazy_static",
+ "num",
+]
+
+[[package]]
+name = "futures-channel"
+version = "0.3.28"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "955518d47e09b25bbebc7a18df10b81f0c766eaf4c4f1cccef2fca5f2a4fb5f2"
+dependencies = [
+ "futures-core",
+]
+
+[[package]]
+name = "futures-core"
+version = "0.3.28"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4bca583b7e26f571124fe5b7561d49cb2868d79116cfa0eefce955557c6fee8c"
+
+[[package]]
+name = "futures-io"
+version = "0.3.28"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4fff74096e71ed47f8e023204cfd0aa1289cd54ae5430a9523be060cdb849964"
+
+[[package]]
+name = "futures-sink"
+version = "0.3.28"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f43be4fe21a13b9781a69afa4985b0f6ee0e1afab2c6f454a8cf30e2b2237b6e"
+
+[[package]]
+name = "futures-task"
+version = "0.3.28"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "76d3d132be6c0e6aa1534069c705a74a5997a356c0dc2f86a47765e5617c5b65"
+
+[[package]]
+name = "futures-util"
+version = "0.3.28"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "26b01e40b772d54cf6c6d721c1d1abd0647a0106a12ecaa1c186273392a69533"
+dependencies = [
+ "futures-core",
+ "futures-io",
+ "futures-task",
+ "memchr",
+ "pin-project-lite",
+ "pin-utils",
+ "slab",
+]
+
+[[package]]
+name = "getrandom"
+version = "0.2.10"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "be4136b2a15dd319360be1c07d9933517ccf0be8f16bf62a3bee4f0d618df427"
+dependencies = [
+ "cfg-if",
+ "js-sys",
+ "libc",
+ "wasi",
+ "wasm-bindgen",
+]
+
+[[package]]
+name = "h2"
+version = "0.3.19"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d357c7ae988e7d2182f7d7871d0b963962420b0678b0997ce7de72001aeab782"
+dependencies = [
+ "bytes",
+ "fnv",
+ "futures-core",
+ "futures-sink",
+ "futures-util",
+ "http",
+ "indexmap",
+ "slab",
+ "tokio",
+ "tokio-util",
+ "tracing",
+]
+
+[[package]]
+name = "hashbrown"
+version = "0.12.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8a9ee70c43aaf417c914396645a0fa852624801b24ebb7ae78fe8272889ac888"
+
[[package]]
name = "hattivatti"
version = "0.1.0"
dependencies = [
+ "anyhow",
+ "clap",
"env_logger",
+ "jsonschema",
"log",
+ "serde",
"serde_json",
+ "url",
+]
+
+[[package]]
+name = "heck"
+version = "0.4.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8"
+
+[[package]]
+name = "hermit-abi"
+version = "0.2.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ee512640fe35acbfb4bb779db6f0d80704c2cacfa2e39b601ef3e3f47d1ae4c7"
+dependencies = [
+ "libc",
]
[[package]]
@@ -72,41 +389,179 @@ version = "0.3.1"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "fed44880c466736ef9a5c5b5facefb5ed0785676d0c02d612db14e54f0d84286"
+[[package]]
+name = "http"
+version = "0.2.9"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "bd6effc99afb63425aff9b05836f029929e345a6148a14b7ecd5ab67af944482"
+dependencies = [
+ "bytes",
+ "fnv",
+ "itoa",
+]
+
+[[package]]
+name = "http-body"
+version = "0.4.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d5f38f16d184e36f2408a55281cd658ecbd3ca05cce6d6510a176eca393e26d1"
+dependencies = [
+ "bytes",
+ "http",
+ "pin-project-lite",
+]
+
+[[package]]
+name = "httparse"
+version = "1.8.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d897f394bad6a705d5f4104762e116a75639e470d80901eed05a860a95cb1904"
+
+[[package]]
+name = "httpdate"
+version = "1.0.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c4a1e36c821dbe04574f602848a19f742f4fb3c98d40449f11bcad18d6b17421"
+
[[package]]
name = "humantime"
version = "2.1.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "9a3a5bfb195931eeb336b2a7b4d761daec841b97f947d34394601737a7bba5e4"
+[[package]]
+name = "hyper"
+version = "0.14.26"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ab302d72a6f11a3b910431ff93aae7e773078c769f0a3ef15fb9ec692ed147d4"
+dependencies = [
+ "bytes",
+ "futures-channel",
+ "futures-core",
+ "futures-util",
+ "h2",
+ "http",
+ "http-body",
+ "httparse",
+ "httpdate",
+ "itoa",
+ "pin-project-lite",
+ "socket2",
+ "tokio",
+ "tower-service",
+ "tracing",
+ "want",
+]
+
+[[package]]
+name = "idna"
+version = "0.4.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7d20d6b07bfbc108882d88ed8e37d39636dcc260e15e30c45e6ba089610b917c"
+dependencies = [
+ "unicode-bidi",
+ "unicode-normalization",
+]
+
+[[package]]
+name = "indexmap"
+version = "1.9.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "bd070e393353796e801d209ad339e89596eb4c8d430d18ede6a1cced8fafbd99"
+dependencies = [
+ "autocfg",
+ "hashbrown",
+]
+
[[package]]
name = "io-lifetimes"
version = "1.0.11"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "eae7b9aee968036d54dce06cebaefd919e4472e753296daccd6d344e3e2df0c2"
dependencies = [
- "hermit-abi",
+ "hermit-abi 0.3.1",
"libc",
"windows-sys",
]
+[[package]]
+name = "ipnet"
+version = "2.7.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "12b6ee2129af8d4fb011108c73d99a1b83a85977f23b82460c0ae2e25bb4b57f"
+
[[package]]
name = "is-terminal"
version = "0.4.7"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "adcf93614601c8129ddf72e2d5633df827ba6551541c6d8c59520a371475be1f"
dependencies = [
- "hermit-abi",
+ "hermit-abi 0.3.1",
"io-lifetimes",
"rustix",
"windows-sys",
]
+[[package]]
+name = "iso8601"
+version = "0.6.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "924e5d73ea28f59011fec52a0d12185d496a9b075d360657aed2a5707f701153"
+dependencies = [
+ "nom",
+]
+
[[package]]
name = "itoa"
version = "1.0.6"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "453ad9f582a441959e5f0d088b02ce04cfe8d51a8eaf077f12ac6d3e94164ca6"
+[[package]]
+name = "js-sys"
+version = "0.3.64"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c5f195fe497f702db0f318b07fdd68edb16955aed830df8363d837542f8f935a"
+dependencies = [
+ "wasm-bindgen",
+]
+
+[[package]]
+name = "jsonschema"
+version = "0.17.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e48354c4c4f088714424ddf090de1ff84acc82b2f08c192d46d226ae2529a465"
+dependencies = [
+ "ahash",
+ "anyhow",
+ "base64",
+ "bytecount",
+ "clap",
+ "fancy-regex",
+ "fraction",
+ "getrandom",
+ "iso8601",
+ "itoa",
+ "memchr",
+ "num-cmp",
+ "once_cell",
+ "parking_lot",
+ "percent-encoding",
+ "regex",
+ "reqwest",
+ "serde",
+ "serde_json",
+ "time",
+ "url",
+ "uuid",
+]
+
+[[package]]
+name = "lazy_static"
+version = "1.4.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646"
+
[[package]]
name = "libc"
version = "0.2.146"
@@ -119,6 +574,16 @@ version = "0.3.8"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "ef53942eb7bf7ff43a617b3e2c1c4a5ecf5944a7c1bc12d7ee39bbb15e5c1519"
+[[package]]
+name = "lock_api"
+version = "0.4.10"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c1cc9717a20b1bb222f333e6a92fd32f7d8a18ddc5a3191a11af45dcbf4dcd16"
+dependencies = [
+ "autocfg",
+ "scopeguard",
+]
+
[[package]]
name = "log"
version = "0.4.19"
@@ -131,6 +596,205 @@ version = "2.5.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "2dffe52ecf27772e601905b7522cb4ef790d2cc203488bbd0e2fe85fcb74566d"
+[[package]]
+name = "mime"
+version = "0.3.17"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6877bb514081ee2a7ff5ef9de3281f14a4dd4bceac4c09388074a6b5df8a139a"
+
+[[package]]
+name = "minimal-lexical"
+version = "0.2.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "68354c5c6bd36d73ff3feceb05efa59b6acb7626617f4962be322a825e61f79a"
+
+[[package]]
+name = "mio"
+version = "0.8.8"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "927a765cd3fc26206e66b296465fa9d3e5ab003e651c1b3c060e7956d96b19d2"
+dependencies = [
+ "libc",
+ "wasi",
+ "windows-sys",
+]
+
+[[package]]
+name = "nom"
+version = "7.1.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d273983c5a657a70a3e8f2a01329822f3b8c8172b73826411a55751e404a0a4a"
+dependencies = [
+ "memchr",
+ "minimal-lexical",
+]
+
+[[package]]
+name = "num"
+version = "0.4.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "43db66d1170d347f9a065114077f7dccb00c1b9478c89384490a3425279a4606"
+dependencies = [
+ "num-bigint",
+ "num-complex",
+ "num-integer",
+ "num-iter",
+ "num-rational",
+ "num-traits",
+]
+
+[[package]]
+name = "num-bigint"
+version = "0.4.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f93ab6289c7b344a8a9f60f88d80aa20032336fe78da341afc91c8a2341fc75f"
+dependencies = [
+ "autocfg",
+ "num-integer",
+ "num-traits",
+]
+
+[[package]]
+name = "num-cmp"
+version = "0.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "63335b2e2c34fae2fb0aa2cecfd9f0832a1e24b3b32ecec612c3426d46dc8aaa"
+
+[[package]]
+name = "num-complex"
+version = "0.4.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "02e0d21255c828d6f128a1e41534206671e8c3ea0c62f32291e808dc82cff17d"
+dependencies = [
+ "num-traits",
+]
+
+[[package]]
+name = "num-integer"
+version = "0.1.45"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "225d3389fb3509a24c93f5c29eb6bde2586b98d9f016636dff58d7c6f7569cd9"
+dependencies = [
+ "autocfg",
+ "num-traits",
+]
+
+[[package]]
+name = "num-iter"
+version = "0.1.43"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7d03e6c028c5dc5cac6e2dec0efda81fc887605bb3d884578bb6d6bf7514e252"
+dependencies = [
+ "autocfg",
+ "num-integer",
+ "num-traits",
+]
+
+[[package]]
+name = "num-rational"
+version = "0.4.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0638a1c9d0a3c0914158145bc76cff373a75a627e6ecbfb71cbe6f453a5a19b0"
+dependencies = [
+ "autocfg",
+ "num-bigint",
+ "num-integer",
+ "num-traits",
+]
+
+[[package]]
+name = "num-traits"
+version = "0.2.15"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "578ede34cf02f8924ab9447f50c28075b4d3e5b269972345e7e0372b38c6cdcd"
+dependencies = [
+ "autocfg",
+]
+
+[[package]]
+name = "num_cpus"
+version = "1.15.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0fac9e2da13b5eb447a6ce3d392f23a29d8694bff781bf03a16cd9ac8697593b"
+dependencies = [
+ "hermit-abi 0.2.6",
+ "libc",
+]
+
+[[package]]
+name = "once_cell"
+version = "1.18.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "dd8b5dd2ae5ed71462c540258bedcb51965123ad7e7ccf4b9a8cafaa4a63576d"
+
+[[package]]
+name = "parking_lot"
+version = "0.12.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3742b2c103b9f06bc9fff0a37ff4912935851bee6d36f3c02bcc755bcfec228f"
+dependencies = [
+ "lock_api",
+ "parking_lot_core",
+]
+
+[[package]]
+name = "parking_lot_core"
+version = "0.9.8"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "93f00c865fe7cabf650081affecd3871070f26767e7b2070a3ffae14c654b447"
+dependencies = [
+ "cfg-if",
+ "libc",
+ "redox_syscall",
+ "smallvec",
+ "windows-targets",
+]
+
+[[package]]
+name = "percent-encoding"
+version = "2.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9b2a4787296e9989611394c33f193f676704af1686e70b8f8033ab5ba9a35a94"
+
+[[package]]
+name = "pin-project-lite"
+version = "0.2.9"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e0a7ae3ac2f1173085d398531c705756c94a4c56843785df85a60c1a0afac116"
+
+[[package]]
+name = "pin-utils"
+version = "0.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8b870d8c151b6f2fb93e84a13146138f05d02ed11c7e7c54f8826aaaf7c9f184"
+
+[[package]]
+name = "proc-macro2"
+version = "1.0.60"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "dec2b086b7a862cf4de201096214fa870344cf922b2b30c167badb3af3195406"
+dependencies = [
+ "unicode-ident",
+]
+
+[[package]]
+name = "quote"
+version = "1.0.28"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1b9ab9c7eadfd8df19006f1cf1a4aed13540ed5cbc047010ece5826e10825488"
+dependencies = [
+ "proc-macro2",
+]
+
+[[package]]
+name = "redox_syscall"
+version = "0.3.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "567664f262709473930a4bf9e51bf2ebf3348f2e748ccc50dea20646858f8f29"
+dependencies = [
+ "bitflags",
+]
+
[[package]]
name = "regex"
version = "1.8.4"
@@ -148,6 +812,40 @@ version = "0.7.2"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "436b050e76ed2903236f032a59761c1eb99e1b0aead2c257922771dab1fc8c78"
+[[package]]
+name = "reqwest"
+version = "0.11.18"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "cde824a14b7c14f85caff81225f411faacc04a2013f41670f41443742b1c1c55"
+dependencies = [
+ "base64",
+ "bytes",
+ "encoding_rs",
+ "futures-core",
+ "futures-util",
+ "h2",
+ "http",
+ "http-body",
+ "hyper",
+ "ipnet",
+ "js-sys",
+ "log",
+ "mime",
+ "once_cell",
+ "percent-encoding",
+ "pin-project-lite",
+ "serde",
+ "serde_json",
+ "serde_urlencoded",
+ "tokio",
+ "tower-service",
+ "url",
+ "wasm-bindgen",
+ "wasm-bindgen-futures",
+ "web-sys",
+ "winreg",
+]
+
[[package]]
name = "rustix"
version = "0.37.20"
@@ -168,11 +866,31 @@ version = "1.0.13"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "f91339c0467de62360649f8d3e185ca8de4224ff281f66000de5eb2a77a79041"
+[[package]]
+name = "scopeguard"
+version = "1.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d29ab0c6d3fc0ee92fe66e2d99f700eab17a8d57d1c1d3b748380fb20baa78cd"
+
[[package]]
name = "serde"
version = "1.0.164"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "9e8c8cf938e98f769bc164923b06dce91cea1751522f46f8466461af04c9027d"
+dependencies = [
+ "serde_derive",
+]
+
+[[package]]
+name = "serde_derive"
+version = "1.0.164"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d9735b638ccc51c28bf6914d90a2e9725b377144fc612c49a611fddd1b631d68"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn",
+]
[[package]]
name = "serde_json"
@@ -185,6 +903,60 @@ dependencies = [
"serde",
]
+[[package]]
+name = "serde_urlencoded"
+version = "0.7.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d3491c14715ca2294c4d6a88f15e84739788c1d030eed8c110436aafdaa2f3fd"
+dependencies = [
+ "form_urlencoded",
+ "itoa",
+ "ryu",
+ "serde",
+]
+
+[[package]]
+name = "slab"
+version = "0.4.8"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6528351c9bc8ab22353f9d776db39a20288e8d6c37ef8cfe3317cf875eecfc2d"
+dependencies = [
+ "autocfg",
+]
+
+[[package]]
+name = "smallvec"
+version = "1.10.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a507befe795404456341dfab10cef66ead4c041f62b8b11bbb92bffe5d0953e0"
+
+[[package]]
+name = "socket2"
+version = "0.4.9"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "64a4a911eed85daf18834cfaa86a79b7d266ff93ff5ba14005426219480ed662"
+dependencies = [
+ "libc",
+ "winapi",
+]
+
+[[package]]
+name = "strsim"
+version = "0.10.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "73473c0e59e6d5812c5dfe2a064a6444949f089e20eec9a2e5506596494e4623"
+
+[[package]]
+name = "syn"
+version = "2.0.18"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "32d41677bcbe24c20c52e7c70b0d8db04134c5d1066bf98662e2871ad200ea3e"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "unicode-ident",
+]
+
[[package]]
name = "termcolor"
version = "1.2.0"
@@ -194,6 +966,250 @@ dependencies = [
"winapi-util",
]
+[[package]]
+name = "time"
+version = "0.3.22"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ea9e1b3cf1243ae005d9e74085d4d542f3125458f3a81af210d901dcd7411efd"
+dependencies = [
+ "serde",
+ "time-core",
+ "time-macros",
+]
+
+[[package]]
+name = "time-core"
+version = "0.1.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7300fbefb4dadc1af235a9cef3737cea692a9d97e1b9cbcd4ebdae6f8868e6fb"
+
+[[package]]
+name = "time-macros"
+version = "0.2.9"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "372950940a5f07bf38dbe211d7283c9e6d7327df53794992d293e534c733d09b"
+dependencies = [
+ "time-core",
+]
+
+[[package]]
+name = "tinyvec"
+version = "1.6.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "87cc5ceb3875bb20c2890005a4e226a4651264a5c75edb2421b52861a0a0cb50"
+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 = "1.28.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "94d7b1cfd2aa4011f2de74c2c4c63665e27a71006b0a192dcd2710272e73dfa2"
+dependencies = [
+ "autocfg",
+ "bytes",
+ "libc",
+ "mio",
+ "num_cpus",
+ "pin-project-lite",
+ "socket2",
+ "windows-sys",
+]
+
+[[package]]
+name = "tokio-util"
+version = "0.7.8"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "806fe8c2c87eccc8b3267cbae29ed3ab2d0bd37fca70ab622e46aaa9375ddb7d"
+dependencies = [
+ "bytes",
+ "futures-core",
+ "futures-sink",
+ "pin-project-lite",
+ "tokio",
+ "tracing",
+]
+
+[[package]]
+name = "tower-service"
+version = "0.3.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b6bc1c9ce2b5135ac7f93c72918fc37feb872bdc6a5533a8b85eb4b86bfdae52"
+
+[[package]]
+name = "tracing"
+version = "0.1.37"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8ce8c33a8d48bd45d624a6e523445fd21ec13d3653cd51f681abf67418f54eb8"
+dependencies = [
+ "cfg-if",
+ "pin-project-lite",
+ "tracing-core",
+]
+
+[[package]]
+name = "tracing-core"
+version = "0.1.31"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0955b8137a1df6f1a2e9a37d8a6656291ff0297c1a97c24e0d8425fe2312f79a"
+dependencies = [
+ "once_cell",
+]
+
+[[package]]
+name = "try-lock"
+version = "0.2.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3528ecfd12c466c6f163363caf2d02a71161dd5e1cc6ae7b34207ea2d42d81ed"
+
+[[package]]
+name = "unicode-bidi"
+version = "0.3.13"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "92888ba5573ff080736b3648696b70cafad7d250551175acbaa4e0385b3e1460"
+
+[[package]]
+name = "unicode-ident"
+version = "1.0.9"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b15811caf2415fb889178633e7724bad2509101cde276048e013b9def5e51fa0"
+
+[[package]]
+name = "unicode-normalization"
+version = "0.1.22"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5c5713f0fc4b5db668a2ac63cdb7bb4469d8c9fed047b1d0292cc7b0ce2ba921"
+dependencies = [
+ "tinyvec",
+]
+
+[[package]]
+name = "url"
+version = "2.4.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "50bff7831e19200a85b17131d085c25d7811bc4e186efdaf54bbd132994a88cb"
+dependencies = [
+ "form_urlencoded",
+ "idna",
+ "percent-encoding",
+]
+
+[[package]]
+name = "utf8parse"
+version = "0.2.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "711b9620af191e0cdc7468a8d14e709c3dcdb115b36f838e601583af800a370a"
+
+[[package]]
+name = "uuid"
+version = "1.3.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0fa2982af2eec27de306107c027578ff7f423d65f7250e40ce0fea8f45248b81"
+
+[[package]]
+name = "version_check"
+version = "0.9.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f"
+
+[[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"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423"
+
+[[package]]
+name = "wasm-bindgen"
+version = "0.2.87"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7706a72ab36d8cb1f80ffbf0e071533974a60d0a308d01a5d0375bf60499a342"
+dependencies = [
+ "cfg-if",
+ "wasm-bindgen-macro",
+]
+
+[[package]]
+name = "wasm-bindgen-backend"
+version = "0.2.87"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5ef2b6d3c510e9625e5fe6f509ab07d66a760f0885d858736483c32ed7809abd"
+dependencies = [
+ "bumpalo",
+ "log",
+ "once_cell",
+ "proc-macro2",
+ "quote",
+ "syn",
+ "wasm-bindgen-shared",
+]
+
+[[package]]
+name = "wasm-bindgen-futures"
+version = "0.4.37"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c02dbc21516f9f1f04f187958890d7e6026df8d16540b7ad9492bc34a67cea03"
+dependencies = [
+ "cfg-if",
+ "js-sys",
+ "wasm-bindgen",
+ "web-sys",
+]
+
+[[package]]
+name = "wasm-bindgen-macro"
+version = "0.2.87"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "dee495e55982a3bd48105a7b947fd2a9b4a8ae3010041b9e0faab3f9cd028f1d"
+dependencies = [
+ "quote",
+ "wasm-bindgen-macro-support",
+]
+
+[[package]]
+name = "wasm-bindgen-macro-support"
+version = "0.2.87"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "54681b18a46765f095758388f2d0cf16eb8d4169b639ab575a8f5693af210c7b"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn",
+ "wasm-bindgen-backend",
+ "wasm-bindgen-shared",
+]
+
+[[package]]
+name = "wasm-bindgen-shared"
+version = "0.2.87"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ca6ad05a4870b2bf5fe995117d3728437bd27d7cd5f06f13c17443ef369775a1"
+
+[[package]]
+name = "web-sys"
+version = "0.3.64"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9b85cbef8c220a6abc02aefd892dfc0fc23afb1c6a426316ec33253a3877249b"
+dependencies = [
+ "js-sys",
+ "wasm-bindgen",
+]
+
[[package]]
name = "winapi"
version = "0.3.9"
@@ -290,3 +1306,12 @@ name = "windows_x86_64_msvc"
version = "0.48.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "1a515f5799fe4961cb532f983ce2b23082366b898e52ffbce459c86f67c8378a"
+
+[[package]]
+name = "winreg"
+version = "0.10.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "80d0f4e272c85def139476380b12f9ac60926689dd2e01d4923222f40580869d"
+dependencies = [
+ "winapi",
+]
diff --git a/Cargo.toml b/Cargo.toml
index 91476f4..5a49a43 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -9,3 +9,8 @@ edition = "2021"
serde_json = "1.0.97"
log = "0.4"
env_logger = "0.10.0"
+serde = { version = "1.0.164", features = ["derive"]}
+jsonschema = "0.17.0"
+url = "2.4.0"
+anyhow = "1.0.71"
+clap = { version = "4.3.4", features = ["derive"] }
diff --git a/src/main.rs b/src/main.rs
index 0b5c42e..843b112 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -1,27 +1,76 @@
use std::fs;
-use std::path::Path;
-use log::{info,warn};
+use std::path::{Path, PathBuf};
+use log::{info, warn};
+use serde::{Deserialize, Serialize};
+use serde_json::{error, Result, Value};
+use serde_json::json;
+
+mod request;
+
+use clap::Parser;
+use crate::request::message::Message;
+
+#[derive(Parser, Debug)]
+#[command(name = "hattivatti")]
+#[command(author = "Benjamin Wingfield <bwingfield@ebi.ac.uk>")]
+#[command(version = "0.1")]
+#[command(about = "Submit pgsc_calc jobs to Puhti")]
+#[command(long_about =
+"This program reads job request messages from the INTERVENE backend and submits a sensitive data
+processing task to the SLURM scheduler. The program also monitors the state of submitted jobs,
+and notifies the INTERVENE backend when a requested job has succeeded or failed.")]
+struct Args {
+ #[arg(short, long)]
+ schema_dir: PathBuf,
+ #[arg(short, long)]
+ message_dir: PathBuf
+}
fn main() {
env_logger::init();
info!("terve! starting up :)");
- let path = Path::new("/Users/bwingfield/Downloads/msgs/msg.jsn");
- let x = read_job_request(&path);
- println!("{}", x.unwrap_or_default());
+ let args = Args::parse();
-}
+ let schema = request::schema::load_schema(args.schema_dir.as_path());
+
+ let m: Message = Message {
+ path: PathBuf::from(Path::new("/Users/bwingfield/Downloads/msgs/invalid_msg.json")),
+ compiled_schema: schema
+ };
-fn read_job_request(file_path: &Path) -> Option<String> {
- return match fs::read_to_string(file_path) {
- Ok(string) => {
- info!("Reading job request: {}", file_path.display());
- Some(string)
- }
- Err(_) => {
- warn!("Can't read job request at path: {}", file_path.display());
- None
- }
- }
+ let x = m.read();
+ println!("Valid serde? {:?}", x.is_some());
+
+
+ // let valid_message = load_message(false);
+ // let result = schema.validate(&valid_message);
+ //
+ // if let Err(errors) = result {
+ // for error in errors {
+ // warn!("Message fails validation");
+ // warn!("Validation error: {}", error);
+ // warn!("Instance path: {}", error.instance_path);
+ // }
+ // } else {
+ // info!("Message passes validation")
+ // }
+
+
+ info!("hattivatti finished")
}
+
+fn load_message(valid: bool) -> Value {
+ let valid_path = Path::new("/Users/bwingfield/Downloads/msgs/valid_msg.json");
+ let invalid_path = Path::new("/Users/bwingfield/Downloads/msgs/invalid_msg.json");
+ let path = if valid {
+ valid_path
+ } else {
+ invalid_path
+ };
+
+ let string_message = fs::read_to_string(&path).expect("File");
+ let message: Value = serde_json::from_str(&string_message).expect("Valid JSON");
+ return message;
+}
\ No newline at end of file
diff --git a/src/request/message.rs b/src/request/message.rs
new file mode 100644
index 0000000..60a7235
--- /dev/null
+++ b/src/request/message.rs
@@ -0,0 +1,109 @@
+use std::{error, fs, io, panic};
+use std::path::{Path, PathBuf};
+
+use jsonschema::{ErrorIterator, JSONSchema, ValidationError};
+use log::{info, warn};
+use serde::{Deserialize, Serialize};
+use serde_json::{Error, Value};
+
+enum MessageError {
+ ValidationFailed,
+ SerializationError,
+ ParseError,
+}
+
+pub struct Message {
+ pub path: PathBuf,
+ pub compiled_schema: JSONSchema,
+}
+
+impl Message {
+ pub fn read(&self) -> Option<JobRequest> {
+ let valid: bool = self.validate().is_ok();
+ if valid {
+ info!("Message is valid");
+ } else {
+ warning!("Message is invalid");
+ }
+ // if validation fails, parsing into strong types will also fail
+ // todo: change from option to Result
+ return self.parse_json();
+ }
+
+ fn validate(&self) -> Result<(), MessageError> {
+ info!("Validating raw message against JSON schema");
+ let job = self.parse_untyped_json().ok_or(MessageError::ParseError)?;
+ let value = serde_json::to_value(&job).map_err(|_| MessageError::SerializationError)?;
+ self.compiled_schema.validate(&value).map_err(|_| MessageError::ValidationFailed)?;
+ Ok(())
+ }
+
+
+ fn read_file(&self) -> Result<String, io::Error> {
+ let path = self.path.as_path();
+ info!("Reading file at {}", path.display());
+ fs::read_to_string(path).map_err(|err| {
+ warn!("Can't read message job request at path {}: {}", path.display(), err);
+ err
+ })
+ }
+
+ fn parse_json(&self) -> Option<JobRequest> {
+ info!("Deserialising JSON into typed Rust object");
+ self.read_file()
+ .ok()
+ .and_then(|string_json| {
+ serde_json::from_str(&string_json).map_err(|err| {
+ warn!("Error parsing JSON: {}", err);
+ }).ok()
+ })
+ }
+
+ fn parse_untyped_json(&self) -> Option<Value> {
+ info!("Parsing JSON into untyped structure");
+ self.read_file()
+ .ok()
+ .and_then(|string_json| {
+ serde_json::from_str(&string_json).map_err(|err| {
+ warn!("Error parsing JSON: {}", err);
+ }).ok()
+ })
+ }
+}
+
+
+#[derive(Debug, Deserialize, Serialize)]
+struct PipelineParam {
+ id: String,
+ target_genomes: Vec<TargetGenome>,
+ nxf_params_file: NxfParamsFile,
+ nxf_work: String,
+}
+
+#[derive(Debug, Deserialize, Serialize)]
+struct TargetGenome {
+ pvar: String,
+ pgen: String,
+ psam: String,
+ sampleset: String,
+ chrom: Option<String>,
+}
+
+#[derive(Debug, Deserialize, Serialize)]
+struct NxfParamsFile {
+ pgs_id: String,
+ format: String,
+ target_build: String,
+}
+
+#[derive(Debug, Deserialize, Serialize)]
+struct GlobusDetails {
+ guest_collection_id: String,
+ dir_path_on_guest_collection: String,
+}
+
+#[derive(Debug, Deserialize, Serialize)]
+pub struct JobRequest {
+ pipeline_param: PipelineParam,
+ globus_details: GlobusDetails,
+}
diff --git a/src/request/schema.rs b/src/request/schema.rs
index 754a5c8..ed20978 100644
--- a/src/request/schema.rs
+++ b/src/request/schema.rs
@@ -4,11 +4,12 @@ use std::sync::Arc;
use anyhow::anyhow;
use jsonschema::{JSONSchema, SchemaResolver, SchemaResolverError};
-use log::warn;
+use log::{info, warn};
use serde_json::{json, Value};
use url::Url;
pub fn load_schema(schema_dir: &Path) -> JSONSchema {
+ info!("Reading schema from {}", schema_dir.display());
let schema_json = read_schema(schema_dir);
compile_schema(&schema_json, schema_dir)
}
@@ -25,6 +26,7 @@ fn read_json_from_path(path: &Path) -> Value {
fn compile_schema(schema: &Value, schema_dir: &Path) -> JSONSchema {
let resolver = LocalResolver { schema_dir: PathBuf::from(schema_dir) };
+ info!("Compiling JSON schema");
JSONSchema::options()
.with_resolver(resolver)
.compile(schema)
--
GitLab