feat: adds wdl-grammar gauntlet for testing grammar parsing

Cargo.toml

@@ -7,6 +7,12 @@ license = "MIT OR Apache-2.0"
 edition = "2021"
 
 [workspace.dependencies]
+clap = { version = "4.4.7", features = ["derive"] }
 env_logger = "0.10.0"
+indexmap = { version = "2.1.0", features = ["serde"] }
 log = "0.4.20"
+pest = { version = "2.7.5", features = ["pretty-print"] }
+pest_derive = "2.7.5"
 serde = { version = "1", features = ["derive"] }
+serde_with = { version = "3.4.0" }
+toml = "0.8.8"

Gauntlet.toml

@@ -0,0 +1,47 @@
+version = "v1"
+
+[[repositories]]
+organization = "PacificBiosciences"
+name = "HiFi-human-WGS-WDL"
+
+[[repositories]]
+organization = "biowdl"
+name = "tasks"
+
+[[repositories]]
+organization = "stjudecloud"
+name = "workflows"
+
+[[repositories]]
+organization = "chanzuckerberg"
+name = "czid-workflows"
+
+[[ignored_errors]]
+document = "biowdl/tasks:bedtools.wdl"
+error = """
+  --> 29:67
+   |
+29 |         String memory = \"~{512 + ceil(size([inputBed, faidx], \"MiB\"))}MiB\"
+   |                                                                   ^---
+   |
+   = expected WHITESPACE or OPTION"""
+
+[[ignored_errors]]
+document = "biowdl/tasks:bowtie.wdl"
+error = """
+  --> 40:58
+   |
+40 |         String memory = \"~{5 + ceil(size(indexFiles, \"GiB\"))}GiB\"
+   |                                                          ^---
+   |
+   = expected WHITESPACE or OPTION"""
+
+[[ignored_errors]]
+document = "stjudecloud/workflows:template/task-templates.wdl"
+error = """
+  --> 17:25
+   |
+17 |         Int memory_gb = <>
+   |                         ^---
+   |
+   = expected WHITESPACE, COMMENT, or expression"""

wdl-grammar/Cargo.toml

@@ -5,9 +5,41 @@ edition.workspace = true
 license.workspace = true
 
 [dependencies]
-clap = { version = "4.4.6", features = ["derive"] }
-env_logger.workspace = true
-log.workspace = true
-pest = "2.7.5"
-pest_derive = "2.7.5"
-serde.workspace = true
+async-recursion = { version = "1.0.5", optional = true }
+chrono = { version = "0.4.31", optional = true }
+clap = { workspace = true, optional = true }
+colored = { version = "2.0.4", optional = true }
+dirs = { version = "5.0.1", optional = true }
+env_logger = { workspace = true, optional = true }
+indexmap = { workspace = true, optional = true }
+log = { workspace = true, optional = true }
+octocrab = { version = "0.32.0", optional = true }
+pest = { workspace = true }
+pest_derive = { workspace = true }
+reqwest = { version = "0.11.22", optional = true }
+serde = { workspace = true }
+serde_with = { workspace = true, optional = true }
+tokio = { version = "1.33.0", features = ["full"], optional = true}
+toml = { workspace = true, optional = true }
+
+[features]
+binaries = [
+    "async-recursion",
+    "chrono",
+    "clap",
+    "colored",
+    "dirs",
+    "env_logger",
+    "indexmap",
+    "log",
+    "octocrab",
+    "reqwest",
+    "serde_with",
+    "tokio",
+    "toml"
+]
+
+[[bin]]
+name = "wdl-grammar"
+path = "src/main.rs"
+required-features = ["binaries"]

wdl-grammar/src/commands.rs

@@ -0,0 +1,38 @@
+//! Subcommands for the `wdl-grammar` command-line tool.
+
+use log::debug;
+
+pub mod create_test;
+pub mod gauntlet;
+pub mod parse;
+
+/// An error common to any subcommand.
+#[derive(Debug)]
+pub enum Error {
+    /// An input/output error.
+    InputOutput(std::io::Error),
+}
+
+impl std::fmt::Display for Error {
+    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
+        match self {
+            Error::InputOutput(err) => write!(f, "i/o error: {err}"),
+        }
+    }
+}
+
+impl std::error::Error for Error {}
+
+/// A [`Result`](std::result::Result) with an [`Error`].
+type Result<T> = std::result::Result<T, Error>;
+
+/// Gets lines of input from STDIN.
+pub fn get_contents_stdin() -> Result<String> {
+    debug!("Reading from STDIN...");
+
+    Ok(std::io::stdin()
+        .lines()
+        .collect::<std::result::Result<Vec<_>, _>>()
+        .map_err(Error::InputOutput)?
+        .join("\n"))
+}