fix: fixes invalid string parsing

Gauntlet.toml

@@ -1,13 +1,5 @@
 version = "v1"
 
-[[repositories]]
-organization = "biowdl"
-name = "tasks"
-
-[[repositories]]
-organization = "chanzuckerberg"
-name = "czid-workflows"
-
 [[repositories]]
 organization = "stjudecloud"
 name = "workflows"
@@ -16,33 +8,25 @@ name = "workflows"
 organization = "PacificBiosciences"
 name = "HiFi-human-WGS-WDL"
 
+[[repositories]]
+organization = "chanzuckerberg"
+name = "czid-workflows"
+
+[[repositories]]
+organization = "biowdl"
+name = "tasks"
+
 [[ignored_errors]]
 document = "biowdl/tasks:bcftools.wdl"
 error = '''validation error: [v1::001] invalid escape character '\_' in string at line 114:75'''
 
 [[ignored_errors]]
 document = "biowdl/tasks:bedtools.wdl"
-error = """
-parse error:
-
-  --> 29:67
-   |
-29 |         String memory = \"~{512 + ceil(size([inputBed, faidx], \"MiB\"))}MiB\"
-   |                                                                   ^---
-   |
-   = expected WHITESPACE or OPTION"""
+error = '''validation error: [v1::001] invalid escape character '\.' in string at line 27:48'''
 
 [[ignored_errors]]
 document = "biowdl/tasks:bowtie.wdl"
-error = """
-parse error:
-
-  --> 40:58
-   |
-40 |         String memory = \"~{5 + ceil(size(indexFiles, \"GiB\"))}GiB\"
-   |                                                          ^---
-   |
-   = expected WHITESPACE or OPTION"""
+error = '''validation error: [v1::001] invalid escape character '\.' in string at line 63:32'''
 
 [[ignored_errors]]
 document = "biowdl/tasks:centrifuge.wdl"

wdl-grammar/src/commands/gauntlet.rs

@@ -89,7 +89,7 @@ pub struct Args {
     quiet: bool,
 
     /// Overwrites the configuration file.
-    #[arg(short, long, global = true)]
+    #[arg(long, global = true)]
     save_config: bool,
 
     /// Silences printing detailed error information.
@@ -101,7 +101,7 @@ pub struct Args {
     skip_remote: bool,
 
     /// Displays warnings as part of the report output.
-    #[arg(short, long, global = true)]
+    #[arg(long, global = true)]
     show_warnings: bool,
 
     /// The Workflow Description Language (WDL) specification version to use.
@@ -307,7 +307,7 @@ pub async fn gauntlet(args: Args) -> Result<()> {
         println!(
             "\n{}\n",
             "Undetected expected errors: you should remove these from your \
-            Config.toml or run this command with the `-s` option!"
+            Config.toml or run this command with the `--save-config` option!"
                 .red()
                 .bold()
         );

wdl-grammar/src/main.rs

@@ -106,3 +106,14 @@ async fn main() {
         Err(err) => eprintln!("error: {}", err),
     }
 }
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn verify_arguments() {
+        use clap::CommandFactory;
+        Args::command().debug_assert()
+    }
+}

wdl-grammar/src/v1/lint/whitespace.rs

@@ -46,6 +46,21 @@ impl Whitespace {
             .try_build()
             .unwrap()
     }
+
+    /// Creates an error corresponding to a line with a trailing tab.
+    fn trailing_tab(&self, line_no: NonZeroUsize) -> lint::Warning
+    where
+        Self: Rule<v1::Rule>,
+    {
+        // SAFETY: this error is written so that it will always unwrap.
+        lint::warning::Builder::default()
+            .code(self.code())
+            .level(lint::Level::Low)
+            .group(lint::Group::Style)
+            .message(format!("trailing tab at the end of line {}", line_no))
+            .try_build()
+            .unwrap()
+    }
 }
 
 impl Rule<v1::Rule> for Whitespace {
@@ -73,6 +88,8 @@ impl Rule<v1::Rule> for Whitespace {
                 results.push(self.empty_line(line_no));
             } else if line.ends_with(' ') {
                 results.push(self.trailing_space(line_no));
+            } else if line.ends_with('\t') {
+                results.push(self.trailing_tab(line_no));
             }
         }
 
@@ -122,14 +139,37 @@ mod tests {
     }
 
     #[test]
-    fn it_unwraps_a_trailing_whitespace_error() {
+    fn it_catches_a_trailing_tab() -> Result<(), Box<dyn std::error::Error>> {
+        let tree = Parser::parse(Rule::document, "version 1.1\t")?;
+        let warning = Whitespace.check(tree)?.unwrap();
+
+        assert_eq!(warning.len(), 1);
+        assert_eq!(
+            warning.first().unwrap().to_string(),
+            "[v1::001::Style/Low] trailing tab at the end of line 1"
+        );
+
+        Ok(())
+    }
+
+    #[test]
+    fn it_unwraps_a_trailing_space_error() {
         let warning = Whitespace.trailing_space(NonZeroUsize::try_from(1).unwrap());
         assert_eq!(
             warning.to_string(),
             "[v1::001::Style/Low] trailing space at the end of line 1"
         )
     }
 
+    #[test]
+    fn it_unwraps_a_trailing_tab_error() {
+        let warning = Whitespace.trailing_tab(NonZeroUsize::try_from(1).unwrap());
+        assert_eq!(
+            warning.to_string(),
+            "[v1::001::Style/Low] trailing tab at the end of line 1"
+        )
+    }
+
     #[test]
     fn it_unwraps_an_empty_line_error() {
         let warning = Whitespace.empty_line(NonZeroUsize::try_from(1).unwrap());

wdl-grammar/src/v1/tests/expression/core.rs

@@ -18,45 +18,49 @@ fn it_successfully_parses_an_array_literal_with_spaces_inside() {
         parser: WdlParser,
         input: "[if a then b else c, \"Hello, world!\"]",
         rule: Rule::core,
-        tokens: [array_literal(0, 37, [
-            expression(1, 19, [
-            r#if(1, 19, [
-                WHITESPACE(3, 4, [
-                    SPACE(3, 4),
-                ]),
-                expression(4, 5, [
-                  identifier(4, 5),
-                ]),
-                WHITESPACE(5, 6, [
-                    SPACE(5, 6),
-                ]),
-                WHITESPACE(10, 11, [
-                    SPACE(10, 11),
-                ]),
-                expression(11, 12, [
-                  identifier(11, 12),
-                ]),
-                WHITESPACE(12, 13, [
-                    SPACE(12, 13),
-                ]),
-                WHITESPACE(17, 18, [
-                    SPACE(17, 18),
+        tokens: [
+            // `[if a then b else c, "Hello, world!"]`
+            array_literal(0, 37, [
+                // `if a then b else c`
+                expression(1, 19, [
+                    // `if a then b else c`
+                    r#if(1, 19, [
+                        WHITESPACE(3, 4, [SPACE(3, 4)]),
+                        // `a`
+                        expression(4, 5, [
+                            // `a`
+                            identifier(4, 5),
+                        ]),
+                        WHITESPACE(5, 6, [SPACE(5, 6)]),
+                        WHITESPACE(10, 11, [SPACE(10, 11)]),
+                        // `b`
+                        expression(11, 12, [
+                            // `b`
+                            identifier(11, 12),
+                        ]),
+                        WHITESPACE(12, 13, [SPACE(12, 13)]),
+                        WHITESPACE(17, 18, [SPACE(17, 18)]),
+                        // `c`
+                        expression(18, 19, [
+                            // `c`
+                            identifier(18, 19),
+                        ]),
+                    ]),
                 ]),
-                expression(18, 19, [
-                  identifier(18, 19),
+                // `,`
+                COMMA(19, 20),
+                WHITESPACE(20, 21, [SPACE(20, 21)]),
+                // `"Hello, world!"`
+                expression(21, 36, [
+                    // `"Hello, world!"`
+                    string(21, 36, [
+                        // `"`
+                        double_quote(21, 22),
+                        // `Hello, world!`
+                        string_literal_contents(22, 35),
+                    ]),
                 ]),
-              ]),
-            ]),
-            COMMA(19, 20),
-            WHITESPACE(20, 21, [
-                SPACE(20, 21),
-            ]),
-            expression(21, 36, [
-              string(21, 36, [
-                double_quoted_string(21, 36),
-              ]),
-            ]),
-          ])
+            ])
         ]
     }
 }