feat: add inconsistent_newlines rule

Gauntlet.toml

@@ -24,7 +24,7 @@ commit_hash = "1e32078d3b57dcb2291534d0caa30f600d40967e"
 
 [repositories."broadinstitute/warp"]
 identifier = "broadinstitute/warp"
-commit_hash = "f094475689311ccf227b39b5f40b70762889566c"
+commit_hash = "77a5d123b4aaf44674d9026149442762826b3687"
 
 [repositories."chanzuckerberg/czid-workflows"]
 identifier = "chanzuckerberg/czid-workflows"
@@ -569,37 +569,37 @@ permalink = "https://github.com/broadinstitute/palantir-workflows/blob/1e32078d3
 [[diagnostics]]
 document = "broadinstitute/warp:/pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl"
 message = "GDCWholeGenomeSomaticSingleSample.wdl:672:14: error: conflicting scatter variable name `ubam`"
-permalink = "https://github.com/broadinstitute/warp/blob/f094475689311ccf227b39b5f40b70762889566c/pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl/#L672"
+permalink = "https://github.com/broadinstitute/warp/blob/77a5d123b4aaf44674d9026149442762826b3687/pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl/#L672"
 
 [[diagnostics]]
 document = "broadinstitute/warp:/pipelines/skylab/scATAC/scATAC.wdl"
 message = "scATAC.wdl:203:9: error: duplicate key `cpu` in runtime section"
-permalink = "https://github.com/broadinstitute/warp/blob/f094475689311ccf227b39b5f40b70762889566c/pipelines/skylab/scATAC/scATAC.wdl/#L203"
+permalink = "https://github.com/broadinstitute/warp/blob/77a5d123b4aaf44674d9026149442762826b3687/pipelines/skylab/scATAC/scATAC.wdl/#L203"
 
 [[diagnostics]]
 document = "broadinstitute/warp:/tasks/broad/GermlineVariantDiscovery.wdl"
 message = "GermlineVariantDiscovery.wdl:137:32: error: expected string, but found integer"
-permalink = "https://github.com/broadinstitute/warp/blob/f094475689311ccf227b39b5f40b70762889566c/tasks/broad/GermlineVariantDiscovery.wdl/#L137"
+permalink = "https://github.com/broadinstitute/warp/blob/77a5d123b4aaf44674d9026149442762826b3687/tasks/broad/GermlineVariantDiscovery.wdl/#L137"
 
 [[diagnostics]]
 document = "broadinstitute/warp:/tasks/broad/GermlineVariantDiscovery.wdl"
 message = "GermlineVariantDiscovery.wdl:65:32: error: expected string, but found integer"
-permalink = "https://github.com/broadinstitute/warp/blob/f094475689311ccf227b39b5f40b70762889566c/tasks/broad/GermlineVariantDiscovery.wdl/#L65"
+permalink = "https://github.com/broadinstitute/warp/blob/77a5d123b4aaf44674d9026149442762826b3687/tasks/broad/GermlineVariantDiscovery.wdl/#L65"
 
 [[diagnostics]]
 document = "broadinstitute/warp:/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl"
 message = "UltimaGenomicsWholeGenomeGermlineTasks.wdl:814:27: error: expected string, but found integer"
-permalink = "https://github.com/broadinstitute/warp/blob/f094475689311ccf227b39b5f40b70762889566c/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl/#L814"
+permalink = "https://github.com/broadinstitute/warp/blob/77a5d123b4aaf44674d9026149442762826b3687/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl/#L814"
 
 [[diagnostics]]
 document = "broadinstitute/warp:/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl"
 message = "UltimaGenomicsWholeGenomeGermlineTasks.wdl:866:27: error: expected string, but found integer"
-permalink = "https://github.com/broadinstitute/warp/blob/f094475689311ccf227b39b5f40b70762889566c/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl/#L866"
+permalink = "https://github.com/broadinstitute/warp/blob/77a5d123b4aaf44674d9026149442762826b3687/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl/#L866"
 
 [[diagnostics]]
 document = "broadinstitute/warp:/tests/cemba/pr/CheckCembaOutputs.wdl"
 message = "CheckCembaOutputs.wdl:1:1: error: a WDL document must start with a version statement"
-permalink = "https://github.com/broadinstitute/warp/blob/f094475689311ccf227b39b5f40b70762889566c/tests/cemba/pr/CheckCembaOutputs.wdl/#L1"
+permalink = "https://github.com/broadinstitute/warp/blob/77a5d123b4aaf44674d9026149442762826b3687/tests/cemba/pr/CheckCembaOutputs.wdl/#L1"
 
 [[diagnostics]]
 document = "chanzuckerberg/czid-workflows:/workflows/index-generation/index-generation.wdl"

wdl-lint/CHANGELOG.md

@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+* Added the `InconsistentNewlines` line rule ([#104](https://github.com/stjude-rust-labs/wdl/pull/104)).
 * Add support for `#@ except` comments to disable lint rules ([#101](https://github.com/stjude-rust-labs/wdl/pull/101)).
 * Added the `LineWidth` lint rule (#99).
 * Added the `ImportWhitespace` and `ImportSort` lint rules (#98).

wdl-lint/RULES.md

@@ -14,7 +14,8 @@ be out of sync with released packages.
 | `ImportPlacement`                | Clarity                       | Ensures that imports are placed between the version statement and any document items. |
 | `ImportSort`                     | Clarity, Style                | Ensures that imports are sorted lexicographically.                                    |
 | `ImportWhitespace`               | Clarity, Style, Spacing       | Ensures that there is no extraneous whitespace between or within imports.             |
-| `InputNotSorted`                 | Style                         | Ensures that input declarations are sorted                 |
+| `InconsistentNewlines`           | Clarity, Style                | Ensures that newlines are used consistently within the file.                          |
+| `InputNotSorted`                 | Style                         | Ensures that input declarations are sorted                                            |
 | `MatchingParameterMeta`          | Completeness                  | Ensures that inputs have a matching entry in a `parameter_meta` section.              |
 | `MissingRuntime`                 | Completeness, Portability     | Ensures that tasks have a runtime section.                                            |
 | `MissingMetas`                   | Completeness, Clarity         | Ensures that tasks have both a meta and a parameter_meta section.                     |

wdl-lint/src/lib.rs

@@ -98,6 +98,7 @@ pub fn rules() -> Vec<Box<dyn Rule>> {
         Box::new(rules::ImportSortRule),
         Box::new(rules::InputNotSortedRule),
         Box::new(rules::LineWidthRule::default()),
+        Box::new(rules::InconsistentNewlinesRule),
     ];
 
     // Ensure all the rule ids are unique and pascal case

wdl-lint/src/rules.rs

@@ -6,6 +6,7 @@ mod ending_newline;
 mod import_placement;
 mod import_sort;
 mod import_whitespace;
+mod inconsistent_newlines;
 mod input_not_sorted;
 mod line_width;
 mod matching_parameter_meta;
@@ -25,6 +26,7 @@ pub use ending_newline::*;
 pub use import_placement::*;
 pub use import_sort::*;
 pub use import_whitespace::*;
+pub use inconsistent_newlines::*;
 pub use input_not_sorted::*;
 pub use line_width::*;
 pub use matching_parameter_meta::*;

wdl-lint/src/rules/inconsistent_newlines.rs

@@ -0,0 +1,96 @@
+//! A lint rule for ensuring that newlines are consistent.
+
+use wdl_ast::AstToken;
+use wdl_ast::Diagnostic;
+use wdl_ast::Diagnostics;
+use wdl_ast::Span;
+use wdl_ast::VisitReason;
+use wdl_ast::Visitor;
+use wdl_ast::Whitespace;
+
+use crate::Rule;
+use crate::Tag;
+use crate::TagSet;
+
+/// The identifier for the inconsistent newlines rule.
+const ID: &str = "InconsistentNewlines";
+
+/// Creates an inconsistent newlines diagnostic.
+fn inconsistent_newlines(span: Span) -> Diagnostic {
+    Diagnostic::note("inconsistent newlines detected")
+        .with_rule(ID)
+        .with_label("the first occurrence of a mismatched newline is here", span)
+        .with_fix("use either \"\\n\" or \"\\r\\n\" consistently in the file")
+}
+
+/// Detects imports that are not sorted lexicographically.
+#[derive(Debug, Clone, Copy)]
+pub struct InconsistentNewlinesRule;
+
+impl Rule for InconsistentNewlinesRule {
+    fn id(&self) -> &'static str {
+        ID
+    }
+
+    fn description(&self) -> &'static str {
+        "Ensures that newline usage is consistent."
+    }
+
+    fn explanation(&self) -> &'static str {
+        "Files should not mix \\n and \\r\\n line breaks. Pick one and use it consistently in your \
+         project."
+    }
+
+    fn tags(&self) -> TagSet {
+        TagSet::new(&[Tag::Style, Tag::Clarity])
+    }
+
+    fn visitor(&self) -> Box<dyn Visitor<State = Diagnostics>> {
+        Box::new(InconsistentNewlinesVisitor::default())
+    }
+}
+
+/// Implements the visitor for the import sort rule.
+struct InconsistentNewlinesVisitor {
+    /// The number of carriage returns in the file.
+    carriage_return: u32,
+    /// The number of newlines in the file.
+    newline: u32,
+    /// Location of first inconsistent newline.
+    first_inconsistent: Option<Span>,
+}
+
+/// Implements the default inconsistent newlines visitor.
+impl Default for InconsistentNewlinesVisitor {
+    fn default() -> Self {
+        Self {
+            carriage_return: 0,
+            newline: 0,
+            first_inconsistent: None,
+        }
+    }
+}
+
+impl Visitor for InconsistentNewlinesVisitor {
+    type State = Diagnostics;
+
+    fn document(&mut self, state: &mut Self::State, reason: VisitReason, _doc: &wdl_ast::Document) {
+        if reason == VisitReason::Exit && self.newline > 0 && self.carriage_return > 0 {
+            state.add(inconsistent_newlines(self.first_inconsistent.unwrap()));
+        }
+    }
+
+    fn whitespace(&mut self, _state: &mut Self::State, whitespace: &Whitespace) {
+        if let Some(pos) = whitespace.as_str().find("\r\n") {
+            self.carriage_return += 1;
+            if self.newline > 0 && self.first_inconsistent.is_none() {
+                self.first_inconsistent = Some(Span::new(whitespace.span().start() + pos, 2));
+            }
+        } else if let Some(pos) = whitespace.as_str().find('\n') {
+            self.newline += 1;
+            if self.carriage_return > 0 && self.first_inconsistent.is_none() {
+                self.first_inconsistent = Some(Span::new(whitespace.span().start() + pos, 1));
+            }
+        }
+    }
+}

wdl-lint/tests/lints.rs

@@ -120,14 +120,13 @@ fn compare_result(path: &Path, result: &str, is_error: bool) -> Result<(), Strin
 
 fn run_test(test: &Path, ntests: &AtomicUsize) -> Result<(), String> {
     let path = test.join("source.wdl");
-    let source = std::fs::read_to_string(&path)
-        .map_err(|e| {
-            format!(
-                "failed to read source file `{path}`: {e}",
-                path = path.display()
-            )
-        })?
-        .replace("\r\n", "\n");
+    let source = std::fs::read_to_string(&path).map_err(|e| {
+        format!(
+            "failed to read source file `{path}`: {e}",
+            path = path.display()
+        )
+    })?;
+
     match Document::parse(&source).into_result() {
         Ok(document) => {
             let mut validator = Validator::default();

wdl-lint/tests/lints/inconsistent-newlines/source.errors

@@ -0,0 +1,9 @@
+note[InconsistentNewlines]: inconsistent newlines detected
+  ┌─ tests/lints/inconsistent-newlines/source.wdl:7:1
+  │  
+7 │ ╭ 
+8 │ │ workflow foo {}
+  │ ╰^ the first occurrence of a mismatched newline is here
+  │  
+  = fix: use either "/n" or "/r/n" consistently in the file
+

wdl-lint/tests/lints/inconsistent-newlines/source.wdl

@@ -0,0 +1,10 @@
+#@ except: EndingNewline,PreambleWhitespace,MissingMetas,MissingOutput
+## This is a test of the `InconsistentNewlines` lint
+## Note that due an inexact path separator replacement in the tests,
+## error messages in the baseline will show `/<escape>` instead of `\<escape>`.
+
+version 1.1
+
+workflow foo {}
+
+