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"zerocopy-derive", +] + +[[package]] +name = "zerocopy-derive" +version = "0.7.35" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e" +dependencies = [ + "proc-macro2", + "quote", + "syn", +] + +[[package]] +name = "zeroize" +version = "1.8.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "ced3678a2879b30306d323f4542626697a464a97c0a07c9aebf7ebca65cd4dde" diff --git a/Cargo.toml b/Cargo.toml new file mode 100644 index 0000000..941af90 --- /dev/null +++ b/Cargo.toml @@ -0,0 +1,63 @@ +[package] +name = "tes" +version = "0.1.0" +edition = "2021" +authors = ["The St. Jude Rust Labs developers"] +license = "MIT OR Apache-2.0" +homepage = "https://github.com/stjude-rust-labs/tes" +repository = "https://github.com/stjude-rust-labs/tes" +rust-version = "1.80.0" + +[dependencies] +anyhow = { version = "1.0.87", optional = true } +chrono = { version = "0.4.38", features = ["serde"] } +ordered-float = { version = "4.2.2", features = ["serde"] } +reqwest = { version = "0.12.7", features = ["json"] } +reqwest-middleware = "0.3.3" +reqwest-retry = "0.6.1" +serde = { version = "1.0.209", features = ["derive"] } +serde_json = "1.0.128" +tokio = { version = "1.40.0", features = ["full", "time"] } +tracing = "0.1.40" +url = { version = "2.5.2", features = ["serde"], optional = true } + +[dev-dependencies] +pretty_assertions = "1.4.0" +tracing-subscriber = { version = "0.3.18", features = ["env-filter"] } + +[features] +default = ["types"] +client = ["dep:anyhow", "types", "dep:url"] +types = ["dep:url"] + +[[example]] +name = "service-info" +required-features = ["client"] + +[[example]] +name = "task-get" +required-features = ["client"] + +[[example]] +name = "task-list-all" +required-features = ["client"] + +[[example]] +name = "task-submit" +required-features = ["client"] + +[lints.rust] +missing_docs = "warn" +nonstandard-style = "warn" +rust-2018-idioms = "warn" +rust-2021-compatibility = "warn" +rust-2024-compatibility = "warn" + +[lints.rustdoc] +broken_intra_doc_links = "warn" + +[lints.clippy] +missing_docs_in_private_items = "warn" + +[package.metadata.docs.rs] +all-features = true diff --git a/LICENSE-APACHE b/LICENSE-APACHE new file mode 100644 index 0000000..0d5b9b2 --- /dev/null +++ b/LICENSE-APACHE @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + +TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + +1. 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+

+ tes +

+ +
+ + CI: Status + + + crates.io version + + crates.io downloads + + License: Apache 2.0 + + + License: MIT + +
+ +
+ A crate for working with the Task Execution Serivice (TES) interface. +
+ +

+ Explore the docs » · + Learn about TES » +

+

+ +## 📚 Getting Started + +The `tes` crate contains types (via the `types` feature) and a simple client +(via the `client` feature) for working with the [Task Execution Service +(TES)][tes-homepage] specification. Briefly, TES is a specification developed to +uniformly submit units of execution ("tasks") to multiple compute environment +through a single HTTP interface. It is of interest mostly when developing +clients or servers that participate in the large-scale submission or monitoring +of jobs. + +To utilize `tes` in your crates, simply add it to your project. + +```bash +# If you want to use the types. +cargo add tes + +# If you also want to use the provided client. +cargo add tes --features client +``` + +After this, you can access the library using the `tes` module in your Rust code. +You can [take a look at the +examples](https://github.com/stjude-rust-labs/tes/tree/main/examples) for +inspiration, but a simple example could look like this. + +```rust +use tes::v1::client; + +#[tokio::main] +async fn main() { + let url = std::env::args().nth(1).expect("url to be present"); + + let client = client::Builder::default() + .url_from_string(url) + .expect("url could not be parsed") + .try_build() + .expect("could not build client"); + + println!( + "{:#?}", + client + .service_info() + .await + .expect("getting service information failed") + ); +} + +``` + +### Minimum Supported Rust Version + +The minimum supported Rust version is currently `1.80.0`. + +There is a CI job that verifies the declared minimum supported version. + +If a contributor submits a PR that uses a feature from a newer version of Rust, +the contributor is responsible for updating the minimum supported version in +the `Cargo.toml`. + +Contributors may update the minimum supported version as-needed to the latest +stable release of Rust. + +To facilitate the discovery of what the minimum supported version should be, +install the `cargo-msrv` tool: + +```bash +cargo install cargo-msrv +``` + +And run the following command: + +```bash +cargo msrv --min 1.80.0 +``` + +If the reported version is newer than the crate's current minimum supported +version, an update is required. + +## 🖥️ Development + +To bootstrap a development environment, please use the following commands. + +```bash +# Clone the repository +git clone git@github.com:stjude-rust-labs/tes.git +cd tes + +# Build the crate in release mode +cargo build --release + +# List out the examples +cargo run --release --example +``` + +## 🚧️ Tests + +Before submitting any pull requests, please make sure the code passes the +following checks (from the root directory). + +```bash +# Run the project's tests. +cargo test --all-features + +# Run the tests for the examples. +cargo test --examples --all-features + +# Ensure the project doesn't have any linting warnings. +cargo clippy --all-features + +# Ensure the project passes `cargo fmt`. +# Currently this requires nightly Rust +cargo +nightly fmt --check + +# Ensure the docs build. +cargo doc +``` + +## 🤝 Contributing + +Contributions, issues and feature requests are welcome! Feel free to check +[issues page](https://github.com/stjude-rust-labs/tes/issues). + +## 📝 License + +This project is licensed as either [Apache 2.0][license-apache] or +[MIT][license-mit] at your discretion. + +Copyright © 2024-Present [St. Jude Children's Research Hospital](https://github.com/stjude). + +[tes-homepage]: https://www.ga4gh.org/product/task-execution-service-tes/ +[license-apache]: https://github.com/stjude-rust-labs/tes/blob/main/LICENSE-APACHE +[license-mit]: https://github.com/stjude-rust-labs/tes/blob/main/LICENSE-MIT diff --git a/docs/FEATURES.md b/docs/FEATURES.md new file mode 100644 index 0000000..5048497 --- /dev/null +++ b/docs/FEATURES.md @@ -0,0 +1,4 @@ +| Feature | Default | Description | +| :----------- | :-----: | :--------------------------------------------------------------- | +| **`client`** | | A simple client that can be used to interact with a TES service. | +| **`types`** | `X` | A representation of all types related to the TES specification. | diff --git a/examples/service-info.rs b/examples/service-info.rs new file mode 100644 index 0000000..9d5ff44 --- /dev/null +++ b/examples/service-info.rs @@ -0,0 +1,39 @@ +//! Gets the descriptive information of the execution service. +//! +//! You can run this with the following command: +//! +//! `TOKEN= RUST_LOG=tes=debug cargo run --release --features=client +//! --example service-info ` + +use anyhow::Context; +use anyhow::Result; +use tes::v1::client; +use tracing_subscriber::EnvFilter; + +#[tokio::main] +async fn main() -> Result<()> { + tracing_subscriber::fmt() + .with_env_filter(EnvFilter::from_default_env()) + .init(); + + let url = std::env::args().nth(1).expect("url to be present"); + + let mut builder = client::Builder::default() + .url_from_string(url) + .expect("url could not be parsed"); + + if let Ok(token) = std::env::var("TOKEN") { + builder = builder.insert_header("Authorization", format!("Basic {}", token)); + } + + let client = builder.try_build().expect("could not build client"); + println!( + "{:#?}", + client + .service_info() + .await + .context("getting the service information")? + ); + + Ok(()) +} diff --git a/examples/simple.rs b/examples/simple.rs new file mode 100644 index 0000000..7c19b19 --- /dev/null +++ b/examples/simple.rs @@ -0,0 +1,26 @@ +//! A simple example of using the client. +//! +//! You can run this with the following command: +//! +//! `cargo run --release --features=client --example simple ` + +use tes::v1::client; + +#[tokio::main] +async fn main() { + let url = std::env::args().nth(1).expect("url to be present"); + + let client = client::Builder::default() + .url_from_string(url) + .expect("url could not be parsed") + .try_build() + .expect("could not build client"); + + println!( + "{:#?}", + client + .service_info() + .await + .expect("getting service information failed") + ); +} diff --git a/examples/task-get.rs b/examples/task-get.rs new file mode 100644 index 0000000..cd4ebed --- /dev/null +++ b/examples/task-get.rs @@ -0,0 +1,42 @@ +//! Gets a particular task within an execution service. +//! +//! You can run this with the following command: +//! +//! `TOKEN= RUST_LOG=tes=debug cargo run --release --features=client +//! --example task-submit ` + +use anyhow::Context; +use anyhow::Result; +use tes::v1::client; +use tes::v1::client::tasks::View; +use tracing_subscriber::EnvFilter; + +#[tokio::main] +async fn main() -> Result<()> { + tracing_subscriber::fmt() + .with_env_filter(EnvFilter::from_default_env()) + .init(); + + let url = std::env::args().nth(1).expect("url to be present"); + let id = std::env::args().nth(2).expect("task id to be present"); + + let mut builder = client::Builder::default() + .url_from_string(url) + .expect("url could not be parsed"); + + if let Ok(token) = std::env::var("TOKEN") { + builder = builder.insert_header("Authorization", format!("Basic {}", token)); + } + + let client = builder.try_build().expect("could not build client"); + + println!( + "{:#?}", + client + .get_task(id, View::Full) + .await + .context("submitting a task")? + ); + + Ok(()) +} diff --git a/examples/task-list-all.rs b/examples/task-list-all.rs new file mode 100644 index 0000000..5ea197a --- /dev/null +++ b/examples/task-list-all.rs @@ -0,0 +1,41 @@ +//! Lists all tasks known about within an execution service. +//! +//! You can run this with the following command: +//! +//! `TOKEN= RUST_LOG=tes=debug cargo run --release --features=client +//! --example task-list-all ` + +use anyhow::Context; +use anyhow::Result; +use tes::v1::client; +use tes::v1::client::tasks::View; +use tracing_subscriber::EnvFilter; + +#[tokio::main] +async fn main() -> Result<()> { + tracing_subscriber::fmt() + .with_env_filter(EnvFilter::from_default_env()) + .init(); + + let url = std::env::args().nth(1).expect("url to be present"); + + let mut builder = client::Builder::default() + .url_from_string(url) + .expect("url could not be parsed"); + + if let Ok(token) = std::env::var("TOKEN") { + builder = builder.insert_header("Authorization", format!("Basic {}", token)); + } + + let client = builder.try_build().expect("could not build client"); + + println!( + "{:#?}", + client + .list_all_tasks(View::Full) + .await + .context("listing all tasks")? + ); + + Ok(()) +} diff --git a/examples/task-submit.rs b/examples/task-submit.rs new file mode 100644 index 0000000..94ff9cb --- /dev/null +++ b/examples/task-submit.rs @@ -0,0 +1,63 @@ +//! Submits an example task to an execution service. +//! +//! You can run this with the following command: +//! +//! `TOKEN= RUST_LOG=tes=debug cargo run --release --features=client +//! --example task-submit ` + +use anyhow::Context; +use anyhow::Result; +use tes::v1::client; +use tes::v1::types::task::Executor; +use tes::v1::types::task::Resources; +use tes::v1::types::Task; +use tracing_subscriber::EnvFilter; + +#[tokio::main] +async fn main() -> Result<()> { + tracing_subscriber::fmt() + .with_env_filter(EnvFilter::from_default_env()) + .init(); + + let url = std::env::args().nth(1).expect("url to be present"); + + let mut builder = client::Builder::default() + .url_from_string(url) + .expect("url could not be parsed"); + + if let Ok(token) = std::env::var("TOKEN") { + builder = builder.insert_header("Authorization", format!("Basic {}", token)); + } + + let client = builder.try_build().expect("could not build client"); + + let task = Task { + name: Some(String::from("my-task")), + description: Some(String::from("A description.")), + resources: Some(Resources { + cpu_cores: Some(4), + preemptible: Some(true), + ..Default::default() + }), + executors: vec![Executor { + image: String::from("ubuntu:latest"), + command: vec![ + String::from("/bin/bash"), + String::from("-c"), + String::from("echo 'hello, world!'"), + ], + ..Default::default() + }], + ..Default::default() + }; + + println!( + "{:#?}", + client + .create_task(task) + .await + .context("submitting a task")? + ); + + Ok(()) +} diff --git a/src/lib.rs b/src/lib.rs new file mode 100644 index 0000000..343356b --- /dev/null +++ b/src/lib.rs @@ -0,0 +1,19 @@ +//! Facilities for working with the Task Execution Service specification. +//! +//! The Task Execution Service (TES) specification is an effort organized by the +//! Global Alliance for Genomics and Health (GA4GH) to define a common API +//! standard for describing and executing batched execution tasks. You can learn +//! more about the specification at the dedicated [website] or the [Swagger +//! Editor][swagger]. +//! +//! At present, versions 1.x of the specification are supported. +//! +//! ## Features +//! +//! This crate provides the following features. +#![doc = include_str!("../docs/FEATURES.md")] +//! [website]: https://ga4gh.github.io/task-execution-schemas/ +//! [swagger]: +//! https://editor.swagger.io/?url=https://ga4gh.github.io/task-execution-schemas/openapi.yaml + +pub mod v1; diff --git a/src/v1.rs b/src/v1.rs new file mode 100644 index 0000000..cc42fd2 --- /dev/null +++ b/src/v1.rs @@ -0,0 +1,10 @@ +//! Facilities related to v1.x of the specification. + +#[cfg(feature = "client")] +pub mod client; + +#[cfg(feature = "client")] +pub use client::Client; + +#[cfg(feature = "types")] +pub mod types; diff --git a/src/v1/client.rs b/src/v1/client.rs new file mode 100644 index 0000000..4fc3efd --- /dev/null +++ b/src/v1/client.rs @@ -0,0 +1,263 @@ +//! A client for interacting with a Task Execution Service (TES) service. + +use reqwest_middleware::ClientWithMiddleware as ReqwestClient; +use serde::Deserialize; +use serde::Serialize; +use tracing::debug; +use tracing::trace; +use url::Url; + +use crate::v1::client::tasks::View; +use crate::v1::types::responses::task; +use crate::v1::types::responses::task::MinimalTask; +use crate::v1::types::responses::CreateTask; +use crate::v1::types::responses::ListTasks; +use crate::v1::types::responses::ServiceInfo; +use crate::v1::types::Task; + +mod builder; +mod options; +pub mod tasks; + +pub use builder::Builder; +pub use options::Options; + +/// An error within the client. +#[derive(Debug)] +pub enum Error { + /// An error when serializing or deserializing JSON. + SerdeJSON(serde_json::Error), + + /// A middleware error from `reqwest_middleware`. + // Note: `reqwest_middleware` stores these as an `anyhow::Error` internally. + Middlware(anyhow::Error), + + /// An error from `reqwest`. + Reqwest(reqwest::Error), +} + +impl std::fmt::Display for Error { + fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result { + match self { + Error::SerdeJSON(err) => write!(f, "json serde error: {err}"), + Error::Middlware(err) => write!(f, "middleware error: {err}"), + Error::Reqwest(err) => write!(f, "reqwest error: {err}"), + } + } +} + +impl std::error::Error for Error {} + +/// A [`Result`](std::result::Result) with an [`Error`]. +type Result = std::result::Result; + +impl From for Error { + fn from(value: reqwest_middleware::Error) -> Self { + match value { + reqwest_middleware::Error::Middleware(err) => Error::Middlware(err), + reqwest_middleware::Error::Reqwest(err) => Error::Reqwest(err), + } + } +} + +/// A client for interacting with a service. +#[derive(Debug)] +pub struct Client { + /// The base URL. + url: Url, + + /// The underlying client. + client: ReqwestClient, +} + +impl Client { + /// Gets an empty builder for a [`Client`]. + pub fn builder() -> Builder { + Builder::default() + } + + /// Performs a `GET` request on an endpoint within the service. + /// + /// # Safety + /// + /// Because calls to `get()` are all local to this crate, the provided + /// `endpoint` is assumed to always be joinable to the base URL without + /// issue. + async fn get(&self, endpoint: impl AsRef) -> Result + where + Response: for<'de> Deserialize<'de>, + { + let endpoint = endpoint.as_ref(); + + // SAFETY: as described in the documentation for this method, the URL is + // already validated upon creationg of the [`Client`], and the + // `endpoint` is assumed to always be joinable to that URL, so this + // should always unwrap. + let url = self.url.join(endpoint).unwrap(); + debug!("GET {url}"); + + let bytes = self + .client + .get(url) + .send() + .await + .map_err(Error::from)? + .bytes() + .await + .map_err(Error::Reqwest)?; + + trace!("{bytes:?}"); + + serde_json::from_slice(&bytes).map_err(Error::SerdeJSON) + } + + /// Performs a `POST1` request on an endpoint within the service. + /// + /// # Safety + /// + /// Because calls to `post()` are all local to this crate, the provided + /// `endpoint` is assumed to always be joinable to the base URL without + /// issue. + async fn post(&self, endpoint: impl AsRef, body: Body) -> Result + where + Body: Serialize, + Response: for<'de> Deserialize<'de>, + { + let endpoint = endpoint.as_ref(); + let body = serde_json::to_string(&body).map_err(Error::SerdeJSON)?; + + // SAFETY: as described in the documentation for this method, the URL is + // already validated upon creationg of the [`Client`], and the + // `endpoint` is assumed to always be joinable to that URL, so this + // should always unwrap. + let url = self.url.join(endpoint).unwrap(); + debug!("POST {url} {body}"); + + self.client + .post(url) + .body(body) + .header("Content-Type", "application/json") + .send() + .await + .map_err(Error::from)? + .json::() + .await + .map_err(Error::Reqwest) + } + + /// Gets the service information. + /// + /// This method makes a request to the `GET /service-info` endpoint. + pub async fn service_info(&self) -> Result { + self.get("./service-info").await + } + + /// Lists a single page of tasks within the service. + /// + /// This method makes a request to the `GET /tasks` endpoint. + pub async fn list_tasks( + &self, + view: &View, + next_token: Option<&str>, + ) -> Result> { + let mut url = format!("./tasks?view={view}"); + + if let Some(token) = next_token { + url.push_str("&page_token="); + url.push_str(token); + } + + match view { + View::Minimal => { + let results = self.get::>(url).await?; + + Ok(ListTasks { + next_page_token: results.next_page_token, + tasks: results + .tasks + .into_iter() + .map(task::Response::Minimal) + .collect::>(), + }) + } + View::Basic => { + let results = self.get::>(url).await?; + + Ok(ListTasks { + next_page_token: results.next_page_token, + tasks: results + .tasks + .into_iter() + .map(task::Response::Basic) + .collect::>(), + }) + } + View::Full => { + let results = self.get::>(url).await?; + + Ok(ListTasks { + next_page_token: results.next_page_token, + tasks: results + .tasks + .into_iter() + .map(task::Response::Full) + .collect::>(), + }) + } + } + } + + /// Lists all tasks within the service. + /// + /// This method is a convenience wrapper around [`Self::list_tasks()`] that + /// submits follow on requests and the server says there are more results. + pub async fn list_all_tasks(&self, view: View) -> Result> { + let mut results = Vec::new(); + let mut next_token = None; + let mut page = 1usize; + + loop { + debug!("reading task page {page} with token {next_token:?}",); + + let response = self.list_tasks(&view, next_token.as_deref()).await?; + results.extend(response.tasks); + + next_token = response.next_page_token; + if next_token.is_none() { + break; + } + + page += 1; + } + + Ok(results) + } + + /// Creates a task within the service. + /// + /// This method makes a request to the `POST /tasks` endpoint. + pub async fn create_task(&self, task: Task) -> Result { + self.post("./tasks", task).await + } + + /// Gets a specific task within the service. + /// + /// This method makes a request to the `GET /tasks/{id}` endpoint. + pub async fn get_task(&self, id: impl AsRef, view: View) -> Result { + let url = format!("./tasks/{}?view={view}", id.as_ref()); + + Ok(match view { + View::Minimal => task::Response::Minimal(self.get(url).await?), + View::Basic => task::Response::Basic(self.get(url).await?), + View::Full => task::Response::Full(self.get(url).await?), + }) + } + + /// Cancels a task within the service. + /// + /// This method makes a request to the `POST /tasks/{id}:cancel` endpoint. + pub async fn cancel_task(&self, id: impl AsRef) -> Result<()> { + self.post(format!("./tasks/{}:cancel", id.as_ref()), ()) + .await + } +} diff --git a/src/v1/client/builder.rs b/src/v1/client/builder.rs new file mode 100644 index 0000000..1b85514 --- /dev/null +++ b/src/v1/client/builder.rs @@ -0,0 +1,130 @@ +//! Builders for a [`Client`]. + +use reqwest::header::HeaderValue; +use reqwest::header::IntoHeaderName; +use reqwest_retry::policies::ExponentialBackoff; +use reqwest_retry::RetryTransientMiddleware; +use url::Url; + +use crate::v1::client::Client; +use crate::v1::client::Options; + +/// An error related to a [`Builder`]. +#[derive(Debug)] +pub enum Error { + /// A required field was missing from the builder. + Missing(&'static str), + + /// An error from `reqwest`. + Reqwest(reqwest::Error), + + /// An error related to a URL. + Url(url::ParseError), +} + +impl std::fmt::Display for Error { + fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result { + match self { + Error::Missing(field) => write!(f, "missing required field: {field}"), + Error::Reqwest(err) => write!(f, "reqwest error: {err}"), + Error::Url(err) => write!(f, "url error: {err}"), + } + } +} + +/// A [`Result`](std::result::Result) with an [`Error`]. +pub type Result = std::result::Result; + +/// A builder for a [`Client`](Client). +#[derive(Debug, Default)] +pub struct Builder { + /// The base URL for the requests. + url: Option, + + /// The options passed to the client. + options: Options, +} + +impl Builder { + /// Adds a base URL to the [`Builder`]. + /// + /// # Notes + /// + /// This will silently overwrite any previous base URL declarations provided + /// to the builder. + pub fn url(mut self, url: impl Into) -> Self { + self.url = Some(url.into()); + self + } + + /// Attempts to parse a URL and add it as the base URL within the + /// [`Builder`]. + /// + /// # Notes + /// + /// This will silently overwrite any previous base URL declarations provided + /// to the builder. + pub fn url_from_string(mut self, url: impl AsRef) -> Result { + self.url = Some(url.as_ref().parse::().map_err(Error::Url)?); + Ok(self) + } + + /// Inserts a default header for the client within the [`Builder`]. + /// + /// # Safety + /// + /// This method assumes that you will pass only values with the following + /// conditions (retrieved from the underlying [`HeaderValue`] code that + /// parses this field): + /// + /// Each character in the value: + /// + /// * must be printable ASCII _AND_ not be the delete character, _OR_ + /// * must be the tab character (`\t`). + /// + /// If your `value` does not conform to this expectation, the function will + /// panic. This design decision was chosen to avoid needing to unwrap in + /// the vast majority of cases. + pub fn insert_header(mut self, key: K, value: impl AsRef) -> Self + where + K: IntoHeaderName, + { + let value = value.as_ref(); + self.options.headers.insert::( + key, + HeaderValue::from_str(value) + .unwrap_or_else(|_| panic!("value for header is not allowed: {value}")), + ); + self + } + + /// Sets the maximum retries for the client within the [`Builder`]. + /// + /// # Notes + /// + /// This will silently overwrite any previous maximum retry declarations + /// provided to the builder. + pub fn retries(mut self, value: u32) -> Self { + self.options.retries = value; + self + } + + /// Consumes `self` and attempts to build a [`Client`] from the provided + /// values. + pub fn try_build(self) -> Result { + let url = self.url.map(Ok).unwrap_or(Err(Error::Missing("url")))?; + + let client = reqwest::ClientBuilder::new() + .default_headers(self.options.headers) + .build() + .map_err(Error::Reqwest)?; + + let client = reqwest_middleware::ClientBuilder::new(client) + .with(RetryTransientMiddleware::new_with_policy( + ExponentialBackoff::builder().build_with_max_retries(self.options.retries), + )) + .build(); + + Ok(Client { url, client }) + } +} diff --git a/src/v1/client/options.rs b/src/v1/client/options.rs new file mode 100644 index 0000000..256a0a4 --- /dev/null +++ b/src/v1/client/options.rs @@ -0,0 +1,25 @@ +//! Options for a [`Client`](super::Client). + +use reqwest::header::HeaderMap; + +/// The number of retries to the server by default. +const DEFAULT_RETRIES: u32 = 3; + +/// Options used within a [`Client`](super::Client). +#[derive(Debug)] +pub struct Options { + /// Headers to include in each request. + pub headers: HeaderMap, + + /// The number of retries per request. + pub retries: u32, +} + +impl Default for Options { + fn default() -> Self { + Self { + headers: Default::default(), + retries: DEFAULT_RETRIES, + } + } +} diff --git a/src/v1/client/tasks.rs b/src/v1/client/tasks.rs new file mode 100644 index 0000000..26f5b79 --- /dev/null +++ b/src/v1/client/tasks.rs @@ -0,0 +1,36 @@ +//! Task-related entities used within a client. + +use serde::Deserialize; +use serde::Serialize; + +/// An argument that affects which fields are returned on certain task-related +/// endpoints. + +#[derive(Debug, Default, Deserialize, Eq, PartialEq, Serialize)] +#[serde(rename_all = "UPPERCASE")] +pub enum View { + /// Only includes the `id` and `state` fields in the returned task. + #[default] + Minimal, + + /// Includes all available fields except: + /// + /// * Logs for stdout (`tesTask.ExecutorLog.stdout`). + /// * Logs for stderr (`tesTask.ExecutorLog.stderr`). + /// * The content of inputs (`tesInput.content`). + /// * The system logs (`tesTaskLog.system_logs`). + Basic, + + /// Includes all fields. + Full, +} + +impl std::fmt::Display for View { + fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result { + match self { + View::Minimal => write!(f, "MINIMAL"), + View::Basic => write!(f, "BASIC"), + View::Full => write!(f, "FULL"), + } + } +} diff --git a/src/v1/types.rs b/src/v1/types.rs new file mode 100644 index 0000000..4e73e51 --- /dev/null +++ b/src/v1/types.rs @@ -0,0 +1,6 @@ +//! Types within v1.x of the specification. + +pub mod responses; +pub mod task; + +pub use task::Task; diff --git a/src/v1/types/responses.rs b/src/v1/types/responses.rs new file mode 100644 index 0000000..954b869 --- /dev/null +++ b/src/v1/types/responses.rs @@ -0,0 +1,25 @@ +//! Responses from a service. + +mod service; +pub mod task; + +use serde::Deserialize; +use serde::Serialize; +pub use service::ServiceInfo; + +/// A response from `POST /tasks`. +#[derive(Debug, Default, Deserialize, Eq, PartialEq, Serialize)] +pub struct CreateTask { + /// The ID of the created task. + pub id: String, +} + +/// The response from `GET /tasks`. +#[derive(Debug, Default, Deserialize, Eq, PartialEq, Serialize)] +pub struct ListTasks { + /// The tasks in this page of results. + pub tasks: Vec, + + /// The token for the next page of results. + pub next_page_token: Option, +} diff --git a/src/v1/types/responses/service.rs b/src/v1/types/responses/service.rs new file mode 100644 index 0000000..89af8ab --- /dev/null +++ b/src/v1/types/responses/service.rs @@ -0,0 +1,194 @@ +//! Responses related to the service itself. + +use chrono::DateTime; +use chrono::Utc; +use serde::Deserialize; +use serde::Serialize; +use url::Url; + +/// Names of specifications supported. +/// +/// Note that, in the case of the Task Execution Service specification, this can +/// only be `"tes"` but it's still technically listed as an enum. +#[derive(Debug, Default, Deserialize, Eq, PartialEq, Serialize)] +pub enum Artifact { + /// A task execution service. + #[serde(rename = "tes")] + #[default] + TaskExecutionService, +} + +/// An organization provided a TES service. +#[derive(Debug, Deserialize, Eq, PartialEq, Serialize)] +pub struct Organization { + /// The organization name. + pub name: String, + + /// A URL for the organization. + pub url: Url, +} + +/// A type of service. +#[derive(Debug, Deserialize, Eq, PartialEq, Serialize)] +pub struct ServiceType { + /// Namespace in reverse domain name format. + pub group: String, + + /// Name of the specification implemented. + pub artifact: Artifact, + + /// The version of the specification being implemented. + pub version: String, +} + +/// A set of service information for the server. +#[derive(Debug, Deserialize, Eq, PartialEq, Serialize)] +#[serde(rename_all = "camelCase")] +pub struct ServiceInfo { + /// A unique identifier for the service. + pub id: String, + + /// Human-readable name of the service. + pub name: String, + + /// The type of the service. + pub r#type: ServiceType, + + /// An optional description of the service. + pub description: Option, + + /// The organization running the service. + pub organization: Organization, + + /// An optional contact URL. + pub contact_url: Option, + + /// An optional documentation URL. + pub documentation_url: Option, + + /// Timestamp when the service was first available. + pub created_at: Option>, + + /// Timestamp when the service was last updated. + pub updated_at: Option>, + + /// An optional string describing the environment that the service is + /// running within. + pub environment: Option, + + /// The version of the service. + pub version: String, + + /// Lists some, but not necessarily all, storage locations supported by the + /// service. + pub storage: Option>, +} + +#[cfg(test)] +mod tests { + use pretty_assertions::assert_eq; + + use super::*; + + #[test] + fn smoke() { + let content = r#"{ + "id": "org.ga4gh.myservice", + "name": "My project", + "type": { + "group": "org.ga4gh", + "artifact": "tes", + "version": "1.0.0" + }, + "description": "This service provides...", + "organization": { + "name": "My organization", + "url": "https://example.com" + }, + "contactUrl": "mailto:support@example.com", + "documentationUrl": "https://docs.myservice.example.com", + "createdAt": "2019-06-04T12:58:19Z", + "updatedAt": "2019-06-04T12:58:19Z", + "environment": "test", + "version": "1.0.0", + "storage": [ + "file:///path/to/local/funnel-storage", + "s3://ohsu-compbio-funnel/storage" + ] +}"#; + + let result: ServiceInfo = serde_json::from_str(content).unwrap(); + + assert_eq!(result.id, "org.ga4gh.myservice"); + assert_eq!(result.name, "My project"); + assert_eq!(result.r#type.group, "org.ga4gh"); + assert_eq!(result.r#type.artifact, Artifact::TaskExecutionService); + assert_eq!(result.r#type.version, "1.0.0"); + assert_eq!(result.description.unwrap(), "This service provides..."); + assert_eq!(result.organization.name, "My organization"); + assert_eq!(result.organization.url.to_string(), "https://example.com/"); + assert_eq!(result.contact_url.unwrap(), "mailto:support@example.com"); + assert_eq!( + result.documentation_url.unwrap().to_string(), + "https://docs.myservice.example.com/" + ); + assert_eq!( + result.created_at.unwrap().to_rfc3339(), + "2019-06-04T12:58:19+00:00" + ); + assert_eq!( + result.updated_at.unwrap().to_rfc3339(), + "2019-06-04T12:58:19+00:00" + ); + assert_eq!(result.environment.unwrap(), "test"); + assert_eq!(result.version, "1.0.0"); + assert_eq!( + result.storage.unwrap(), + vec![ + "file:///path/to/local/funnel-storage", + "s3://ohsu-compbio-funnel/storage" + ] + ); + } + + #[test] + fn full_conversion() { + let now = DateTime::parse_from_rfc3339("2024-09-07T20:27:35.345673Z") + .unwrap() + .into(); + + let info = ServiceInfo { + id: String::from("org.ga4gh.myservice"), + name: String::from("My Server"), + r#type: ServiceType { + group: String::from("org.ga4gh"), + artifact: Artifact::TaskExecutionService, + version: String::from("1.0.0"), + }, + description: Some(String::from("A description")), + organization: Organization { + name: String::from("My Organization"), + url: Url::try_from("https://example.com").unwrap(), + }, + contact_url: Some(String::from("mailto:foo@bar.com")), + documentation_url: Some(Url::try_from("https://docs.myservice.example.com").unwrap()), + created_at: Some(now), + updated_at: Some(now), + environment: Some(String::from("test")), + version: String::from("1.5.0"), + storage: Some(vec![ + String::from("file:///path/to/local/funnel-storage"), + String::from("s3://ohsu-compbio-funnel/storage"), + ]), + }; + + let serialized = serde_json::to_string(&info).unwrap(); + assert_eq!( + serialized, + r#"{"id":"org.ga4gh.myservice","name":"My Server","type":{"group":"org.ga4gh","artifact":"tes","version":"1.0.0"},"description":"A description","organization":{"name":"My Organization","url":"https://example.com/"},"contactUrl":"mailto:foo@bar.com","documentationUrl":"https://docs.myservice.example.com/","createdAt":"2024-09-07T20:27:35.345673Z","updatedAt":"2024-09-07T20:27:35.345673Z","environment":"test","version":"1.5.0","storage":["file:///path/to/local/funnel-storage","s3://ohsu-compbio-funnel/storage"]}"# + ); + + let deserialized: ServiceInfo = serde_json::from_str(&serialized).unwrap(); + assert_eq!(info, deserialized); + } +} diff --git a/src/v1/types/responses/task.rs b/src/v1/types/responses/task.rs new file mode 100644 index 0000000..3f673bc --- /dev/null +++ b/src/v1/types/responses/task.rs @@ -0,0 +1,73 @@ +//! Responses related to tasks. + +use serde::Deserialize; +use serde::Serialize; + +use crate::v1::types::task::State; +use crate::v1::types::Task; + +/// A response for when `?view=MINIMAL` in a task endpoint. +#[derive(Debug, Default, Deserialize, Eq, PartialEq, Serialize)] +pub struct MinimalTask { + /// The ID. + pub id: String, + + /// The current state. + pub state: Option, +} + +/// A generalized response for getting tasks with the `view` parameter. +#[derive(Debug, Deserialize, Eq, PartialEq, Serialize)] +#[serde(untagged)] +pub enum Response { + /// A response for when `?view=MINIMAL` in a task endpoint. + Minimal(MinimalTask), + + /// A response for when `?view=BASIC` in a task endpoint. + /// + /// **NOTE:** all of the fields that are optional in the specification for + /// this response are also optional on [`Task`], so we can reuse this + /// struct here instead of subsetting it. + Basic(Task), + + /// A response for when `?view=FULL` in a task endpoint. + Full(Task), +} + +impl Response { + /// Retrieves a reference to the inner [`Minimal`] response if the variant + /// is [`Response::Minimal`]. + pub fn as_minimal(&self) -> Option<&MinimalTask> { + match self { + Response::Minimal(task) => Some(task), + _ => None, + } + } + + /// Consumes `self` and returns the inner [`Minimal`] response if the + /// variant is [`Response::Minimal`]. + pub fn into_minimal(self) -> Option { + match self { + Response::Minimal(task) => Some(task), + _ => None, + } + } + + /// Retrieves a reference to the inner [`Task`] response if the variant + /// is [`Response::Basic`] or [`Response::Full`]. + pub fn as_task(&self) -> Option<&Task> { + match self { + Response::Basic(task) | Response::Full(task) => Some(task), + _ => None, + } + } + + /// Consumes `self` and returns the inner [`Task`] response if the variant + /// is [`Response::Basic`] or [`Response::Full`]. + pub fn into_task(self) -> Option { + match self { + Response::Basic(task) | Response::Full(task) => Some(task), + _ => None, + } + } +} diff --git a/src/v1/types/task.rs b/src/v1/types/task.rs new file mode 100644 index 0000000..47909e9 --- /dev/null +++ b/src/v1/types/task.rs @@ -0,0 +1,199 @@ +//! Tasks submitted to a service. + +use std::collections::HashMap; + +use chrono::DateTime; +use chrono::Utc; +use ordered_float::OrderedFloat; +use serde::Deserialize; +use serde::Serialize; + +pub mod executor; +pub mod file; + +pub use executor::Executor; + +/// State of TES task. +#[derive(Debug, Default, Deserialize, Eq, PartialEq, Serialize)] +pub enum State { + /// An unknown state. + #[serde(rename = "UNKNOWN")] + #[default] + Unknown, + + /// A queued task. + #[serde(rename = "QUEUED")] + Queued, + + /// A task that is initializing. + #[serde(rename = "INITIALIZING")] + Initializing, + + /// A task that is running. + #[serde(rename = "RUNNING")] + Running, + + /// A task that is paused. + #[serde(rename = "PAUSED")] + Paused, + + /// A task that has completed. + #[serde(rename = "COMPLETE")] + Complete, + + /// A task that has errored during execution. + #[serde(rename = "EXECUTOR_ERROR")] + ExecutorError, + + /// A task that has encountered a system error. + #[serde(rename = "SYSTEM_ERROR")] + SystemError, + + /// A task that has been cancelled. + #[serde(rename = "CANCELED")] + Canceled, +} + +impl State { + /// Returns whether a task is still executing or not. + pub fn is_executing(&self) -> bool { + matches!( + self, + Self::Unknown | Self::Queued | Self::Initializing | Self::Running | Self::Paused + ) + } +} + +/// An input for a TES task. +#[derive(Debug, Default, Deserialize, Eq, PartialEq, Serialize)] +pub struct Input { + /// An optional name. + pub name: Option, + + /// An optional description. + pub description: Option, + + /// An optional URL. + pub url: Option, + + /// Where the input will be mounted within the container. + pub path: String, + + /// The type. + #[serde(rename = "type")] + pub r#type: file::Type, + + /// The content. + pub content: Option, +} + +/// An output for a TES task. +#[derive(Debug, Default, Deserialize, Eq, PartialEq, Serialize)] +pub struct Output { + /// An optional name. + pub name: Option, + + /// An optional description. + pub description: Option, + + /// The URL where the result will be stored. + pub url: String, + + /// The path to the output within the container. + pub path: String, + + /// The type. + #[serde(rename = "type")] + pub r#type: file::Type, +} + +/// Requested resources for a TES task. +#[derive(Debug, Default, Deserialize, Eq, PartialEq, Serialize)] +pub struct Resources { + /// The number of CPU cores. + pub cpu_cores: Option, + + /// Whether or not the task prefers to be preemptible. + pub preemptible: Option, + + /// The amount of RAM (in gigabytes). + pub ram_gb: Option>, + + /// The amount of disk space (in gigabytes). + pub disk_gb: Option>, + + /// The zones. + pub zones: Option>, +} + +/// An output file log. +#[derive(Debug, Default, Deserialize, Eq, PartialEq, Serialize)] +pub struct OutputFileLog { + /// The URL. + pub url: String, + + /// The path within the container. + pub path: String, + + /// The size in bytes. + pub size_bytes: String, +} + +/// A task log. +#[derive(Debug, Default, Deserialize, Eq, PartialEq, Serialize)] +pub struct TaskLog { + /// The executor logs. + pub logs: Vec, + + /// The start time. + pub start_time: Option>, + + /// The end time. + pub end_time: Option>, + + /// The output file logs. + pub outputs: Option>, + + /// The system logs. + pub system_logs: Option>, +} + +/// A task. +#[derive(Debug, Default, Deserialize, Eq, PartialEq, Serialize)] +pub struct Task { + /// The ID. + pub id: Option, + + /// The current state. + pub state: Option, + + /// The user-provided name. + pub name: Option, + + /// The user-provided description. + pub description: Option, + + /// The inputs. + pub inputs: Option>, + + /// The outputs. + pub outputs: Option>, + + /// The requested resources. + pub resources: Option, + + /// The executors. + pub executors: Vec, + + /// The volumes. + pub volumes: Option>, + + /// The tags. + pub tags: Option>, + + /// The logs. + pub logs: Option>, + + /// The time of creation. + pub creation_time: Option>, +} diff --git a/src/v1/types/task/executor.rs b/src/v1/types/task/executor.rs new file mode 100644 index 0000000..794fd9f --- /dev/null +++ b/src/v1/types/task/executor.rs @@ -0,0 +1,56 @@ +//! Executor declared within tasks. + +use std::collections::HashMap; + +use chrono::DateTime; +use chrono::Utc; +use serde::Deserialize; +use serde::Serialize; + +/// An executor. +/// +/// In short, an executor is a single command that is run in a different +/// container image. [`Executor`]s are run sequentially as they are specified in +/// the task. +#[derive(Debug, Default, Deserialize, Eq, PartialEq, Serialize)] +pub struct Executor { + /// The image. + pub image: String, + + /// The command. + pub command: Vec, + + /// The working directory. + pub workdir: Option, + + /// The path from which to pipe the standard input stream. + pub stdin: Option, + + /// The path to pipe the standard output stream to. + pub stdout: Option, + + /// The path to pipe the standard error stream to. + pub stderr: Option, + + /// The environment variables. + pub env: Option>, +} + +/// A log for an [`Executor`]. +#[derive(Debug, Default, Deserialize, Eq, PartialEq, Serialize)] +pub struct Log { + /// The start time. + pub start_time: Option>, + + /// The end time. + pub end_time: Option>, + + /// The value of the standard output stream. + pub stdout: Option, + + /// The value of the standard error stream. + pub stderr: Option, + + /// The exit code. + pub exit_code: Option, +} diff --git a/src/v1/types/task/file.rs b/src/v1/types/task/file.rs new file mode 100644 index 0000000..f4b67f0 --- /dev/null +++ b/src/v1/types/task/file.rs @@ -0,0 +1,17 @@ +//! Files declared within tasks. + +use serde::Deserialize; +use serde::Serialize; + +/// A type of file. +#[derive(Debug, Default, Deserialize, Eq, PartialEq, Serialize)] +pub enum Type { + /// A file. + #[serde(rename = "FILE")] + #[default] + File, + + /// A directory. + #[serde(rename = "DIRECTORY")] + Directory, +}