feat: implement the file functions from the WDL standard library.

Cargo.toml

@@ -33,6 +33,7 @@ dirs = "5.0.1"
 faster-hex = "0.9.0"
 futures = "0.3.30"
 git2 = "0.18.3"
+glob = "0.3.1"
 id-arena = "2.2.1"
 indexmap = { version = "2.2.6", features = ["serde"] }
 indicatif = "0.17.8"

gauntlet/src/lib.rs

@@ -312,7 +312,7 @@ pub async fn gauntlet(args: Args) -> Result<()> {
             };
 
             report
-                .register(document_identifier, status, elapsed)
+                .register(document_identifier, status)
                 .context("failed to register report status")?;
         }
 
@@ -330,7 +330,7 @@ pub async fn gauntlet(args: Args) -> Result<()> {
             .next_section()
             .context("failed to transition to next report section")?;
         report
-            .footer(repository_identifier)
+            .footer(repository_identifier, elapsed)
             .context("failed to write report footer")?;
         report
             .next_section()

gauntlet/src/report.rs

@@ -176,7 +176,6 @@ impl<T: std::io::Write> Report<T> {
         &mut self,
         identifier: document::Identifier,
         status: Status,
-        elapsed: Duration,
     ) -> std::io::Result<()> {
         if self.section != Section::Summary {
             panic!(
@@ -185,7 +184,7 @@ impl<T: std::io::Write> Report<T> {
             );
         }
 
-        writeln!(self.inner, "{status} {identifier} ({elapsed:?})")?;
+        writeln!(self.inner, "{status} {identifier}")?;
         self.results.insert(identifier, status);
         self.printed = true;
 
@@ -238,6 +237,7 @@ impl<T: std::io::Write> Report<T> {
     pub fn footer(
         &mut self,
         repository_identifier: &repository::Identifier,
+        elapsed: Duration,
     ) -> std::io::Result<()> {
         if self.section != Section::Footer {
             panic!(
@@ -292,7 +292,7 @@ impl<T: std::io::Write> Report<T> {
 
         writeln!(
             self.inner,
-            " ({:.1}%)",
+            " ({:.1}%) analyzed in {elapsed:?}",
             (passed as f64 / considered as f64) * 100.0
         )?;
         self.printed = true;

wdl-analysis/src/stdlib.rs

@@ -1651,14 +1651,22 @@ pub struct StandardLibrary {
     types: Types,
     /// A map of function name to function definition.
     functions: IndexMap<&'static str, Function>,
-    /// The type for `Array[String]`.
-    pub(crate) array_string: Type,
     /// The type for `Array[Int]`.
-    pub(crate) array_int: Type,
-    /// The type for `Map[String, Int]`.
-    pub(crate) map_string_int: Type,
+    array_int: Type,
+    /// The type for `Array[String]`.
+    array_string: Type,
+    /// The type for `Array[File]`.
+    array_file: Type,
+    /// The type for `Array[Object]`.
+    array_object: Type,
+    /// The type for `Array[String]+`.
+    array_string_non_empty: Type,
+    /// The type for `Array[Array[String]]`.
+    array_array_string: Type,
     /// The type for `Map[String, String]`.
-    pub(crate) map_string_string: Type,
+    map_string_string: Type,
+    /// The type for `Map[String, Int]`.
+    map_string_int: Type,
 }
 
 impl StandardLibrary {
@@ -1676,6 +1684,46 @@ impl StandardLibrary {
     pub fn functions(&self) -> impl ExactSizeIterator<Item = (&'static str, &Function)> {
         self.functions.iter().map(|(n, f)| (*n, f))
     }
+
+    /// Gets the type for `Array[Int]`.
+    pub fn array_int_type(&self) -> Type {
+        self.array_int
+    }
+
+    /// Gets the type for `Array[String]`.
+    pub fn array_string_type(&self) -> Type {
+        self.array_string
+    }
+
+    /// Gets the type for `Array[File]`.
+    pub fn array_file_type(&self) -> Type {
+        self.array_file
+    }
+
+    /// Gets the type for `Array[Object]`.
+    pub fn array_object_type(&self) -> Type {
+        self.array_object
+    }
+
+    /// Gets the type for `Array[String]+`.
+    pub fn array_string_non_empty_type(&self) -> Type {
+        self.array_string_non_empty
+    }
+
+    /// Gets the type for `Array[Array[String]]`.
+    pub fn array_array_string_type(&self) -> Type {
+        self.array_array_string
+    }
+
+    /// Gets the type for `Map[String, String]`.
+    pub fn map_string_string_type(&self) -> Type {
+        self.map_string_string
+    }
+
+    /// Gets the type for `Map[String, Int]`.
+    pub fn map_string_int_type(&self) -> Type {
+        self.map_string_int
+    }
 }
 
 /// Represents the WDL standard library.
@@ -1958,6 +2006,15 @@ pub static STDLIB: LazyLock<StandardLibrary> = LazyLock::new(|| {
             .insert(
                 "size",
                 PolymorphicFunction::new(vec![
+                    // This overload isn't explicitly in the spec, but it fixes an ambiguity in 1.2
+                    // when passed a literal `None` value.
+                    FunctionSignature::builder()
+                        .min_version(SupportedVersion::V1(V1::Two))
+                        .required(1)
+                        .parameter(Type::None)
+                        .parameter(PrimitiveTypeKind::String)
+                        .ret(PrimitiveTypeKind::Float)
+                        .build(),
                     FunctionSignature::builder()
                         .required(1)
                         .parameter(PrimitiveType::optional(PrimitiveTypeKind::File))
@@ -1969,6 +2026,7 @@ pub static STDLIB: LazyLock<StandardLibrary> = LazyLock::new(|| {
                     // `String` overload is required as `String` may coerce to either `File` or
                     // `Directory`, which is ambiguous.
                     FunctionSignature::builder()
+                        .min_version(SupportedVersion::V1(V1::Two))
                         .required(1)
                         .parameter(PrimitiveType::optional(PrimitiveTypeKind::String))
                         .parameter(PrimitiveTypeKind::String)
@@ -2131,11 +2189,13 @@ pub static STDLIB: LazyLock<StandardLibrary> = LazyLock::new(|| {
                         .ret(array_array_string)
                         .build(),
                     FunctionSignature::builder()
+                        .min_version(SupportedVersion::V1(V1::Two))
                         .parameter(PrimitiveTypeKind::File)
                         .parameter(PrimitiveTypeKind::Boolean)
                         .ret(array_object)
                         .build(),
                     FunctionSignature::builder()
+                        .min_version(SupportedVersion::V1(V1::Two))
                         .parameter(PrimitiveTypeKind::File)
                         .parameter(PrimitiveTypeKind::Boolean)
                         .parameter(array_string)
@@ -2158,18 +2218,16 @@ pub static STDLIB: LazyLock<StandardLibrary> = LazyLock::new(|| {
                         .ret(PrimitiveTypeKind::File)
                         .build(),
                     FunctionSignature::builder()
-                        .type_parameter("S", StructConstraint)
-                        .parameter(GenericArrayType::new(GenericType::Parameter("S")))
-                        .ret(PrimitiveTypeKind::File)
-                        .build(),
-                    FunctionSignature::builder()
+                        .min_version(SupportedVersion::V1(V1::Two))
                         .parameter(array_array_string)
                         .parameter(PrimitiveTypeKind::Boolean)
                         .parameter(array_string)
                         .ret(PrimitiveTypeKind::File)
                         .build(),
                     FunctionSignature::builder()
-                        .type_parameter("S", StructConstraint)
+                        .min_version(SupportedVersion::V1(V1::Two))
+                        .type_parameter("S", PrimitiveStructConstraint)
+                        .required(1)
                         .parameter(GenericArrayType::new(GenericType::Parameter("S")))
                         .parameter(PrimitiveTypeKind::Boolean)
                         .parameter(array_string)
@@ -2289,7 +2347,8 @@ pub static STDLIB: LazyLock<StandardLibrary> = LazyLock::new(|| {
                         .ret(PrimitiveTypeKind::File)
                         .build(),
                     FunctionSignature::builder()
-                        .type_parameter("S", StructConstraint)
+                        .min_version(SupportedVersion::V1(V1::One))
+                        .type_parameter("S", PrimitiveStructConstraint)
                         .parameter(GenericType::Parameter("S"))
                         .ret(PrimitiveTypeKind::File)
                         .build(),
@@ -2310,7 +2369,8 @@ pub static STDLIB: LazyLock<StandardLibrary> = LazyLock::new(|| {
                         .ret(PrimitiveTypeKind::File)
                         .build(),
                     FunctionSignature::builder()
-                        .type_parameter("S", StructConstraint)
+                        .min_version(SupportedVersion::V1(V1::One))
+                        .type_parameter("S", PrimitiveStructConstraint)
                         .parameter(GenericArrayType::new(GenericType::Parameter("S")))
                         .ret(PrimitiveTypeKind::File)
                         .build(),
@@ -2853,10 +2913,14 @@ pub static STDLIB: LazyLock<StandardLibrary> = LazyLock::new(|| {
     StandardLibrary {
         types,
         functions,
-        array_string,
         array_int,
-        map_string_int,
+        array_string,
+        array_file,
+        array_object,
+        array_string_non_empty,
+        array_array_string,
         map_string_string,
+        map_string_int,
     }
 });
 
@@ -2912,6 +2976,7 @@ mod test {
             "join_paths(File, Array[String]+) -> File",
             "join_paths(Array[String]+) -> File",
             "glob(String) -> Array[File]",
+            "size(None, <String>) -> Float",
             "size(File?, <String>) -> Float",
             "size(String?, <String>) -> Float",
             "size(Directory?, <String>) -> Float",
@@ -2929,19 +2994,20 @@ mod test {
             "read_tsv(File, Boolean) -> Array[Object]",
             "read_tsv(File, Boolean, Array[String]) -> Array[Object]",
             "write_tsv(Array[Array[String]]) -> File",
-            "write_tsv(Array[S]) -> File where `S`: any structure",
             "write_tsv(Array[Array[String]], Boolean, Array[String]) -> File",
-            "write_tsv(Array[S], Boolean, Array[String]) -> File where `S`: any structure",
+            "write_tsv(Array[S], <Boolean>, <Array[String]>) -> File where `S`: any structure \
+             containing only primitive types",
             "read_map(File) -> Map[String, String]",
             "write_map(Map[String, String]) -> File",
             "read_json(File) -> Union",
             "write_json(X) -> File where `X`: any JSON-serializable type",
             "read_object(File) -> Object",
             "read_objects(File) -> Array[Object]",
             "write_object(Object) -> File",
-            "write_object(S) -> File where `S`: any structure",
+            "write_object(S) -> File where `S`: any structure containing only primitive types",
             "write_objects(Array[Object]) -> File",
-            "write_objects(Array[S]) -> File where `S`: any structure",
+            "write_objects(Array[S]) -> File where `S`: any structure containing only primitive \
+             types",
             "prefix(String, Array[P]) -> Array[String] where `P`: any required primitive type",
             "suffix(String, Array[P]) -> Array[String] where `P`: any required primitive type",
             "quote(Array[P]) -> Array[String] where `P`: any required primitive type",

wdl-analysis/src/stdlib/constraints.rs

@@ -2,6 +2,7 @@
 
 use std::fmt;
 
+use crate::types::Coercible;
 use crate::types::CompoundType;
 use crate::types::CompoundTypeDef;
 use crate::types::Optional;
@@ -114,6 +115,27 @@ impl Constraint for StructConstraint {
     }
 }
 
+/// Represents a constraint that ensures the type is any structure that contains
+/// only primitive types.
+#[derive(Debug, Copy, Clone)]
+pub struct PrimitiveStructConstraint;
+
+impl Constraint for PrimitiveStructConstraint {
+    fn description(&self) -> &'static str {
+        "any structure containing only primitive types"
+    }
+
+    fn satisfied(&self, types: &Types, ty: Type) -> bool {
+        if let Type::Compound(ty) = ty {
+            if let CompoundTypeDef::Struct(s) = types.type_definition(ty.definition()) {
+                return s.members().values().all(|ty| ty.as_primitive().is_some());
+            }
+        }
+
+        false
+    }
+}
+
 /// Represents a constraint that ensures the type is JSON serializable.
 #[derive(Debug, Copy, Clone)]
 pub struct JsonSerializableConstraint;
@@ -130,8 +152,8 @@ impl Constraint for JsonSerializableConstraint {
                 CompoundTypeDef::Array(ty) => type_is_serializable(types, ty.element_type()),
                 CompoundTypeDef::Pair(_) => false,
                 CompoundTypeDef::Map(ty) => {
-                    !ty.key_type().is_optional()
-                        && matches!(ty.key_type(), Type::Primitive(ty) if ty.kind() == PrimitiveTypeKind::String)
+                    ty.key_type()
+                        .is_coercible_to(types, &PrimitiveTypeKind::String.into())
                         && type_is_serializable(types, ty.value_type())
                 }
                 CompoundTypeDef::Struct(s) => s