feat: add non-matching output lint rule

Arena.toml

@@ -1257,7 +1257,7 @@ permalink = "https://github.com/stjudecloud/workflows/blob/efdca837bc35fe5647de6
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/tools/fq.wdl"
-message = "fq.wdl:91:9: warning[NonmatchingOutput]: output `check` is missing from `meta` section in task `fqlint`"
+message = "fq.wdl:91:9: warning[NonmatchingOutput]: output `check` is missing from `meta.outputs` section in task `fqlint`"
 permalink = "https://github.com/stjudecloud/workflows/blob/efdca837bc35fe5647de6aa95989652a5a9648dc/tools/fq.wdl/#L91"
 
 [[diagnostics]]
@@ -1332,7 +1332,7 @@ permalink = "https://github.com/stjudecloud/workflows/blob/efdca837bc35fe5647de6
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/tools/ngsderive.wdl"
-message = "ngsderive.wdl:133:9: warning[NonmatchingOutput]: output `instrument_string` is missing from `meta` section in task `instrument`"
+message = "ngsderive.wdl:133:9: warning[NonmatchingOutput]: output `instrument_string` is missing from `meta.outputs` section in task `instrument`"
 permalink = "https://github.com/stjudecloud/workflows/blob/efdca837bc35fe5647de6aa95989652a5a9648dc/tools/ngsderive.wdl/#L133"
 
 [[diagnostics]]
@@ -1352,7 +1352,7 @@ permalink = "https://github.com/stjudecloud/workflows/blob/efdca837bc35fe5647de6
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/tools/ngsderive.wdl"
-message = "ngsderive.wdl:80:9: warning[NonmatchingOutput]: output `strandedness_string` is missing from `meta` section in task `strandedness`"
+message = "ngsderive.wdl:80:9: warning[NonmatchingOutput]: output `strandedness_string` is missing from `meta.outputs` section in task `strandedness`"
 permalink = "https://github.com/stjudecloud/workflows/blob/efdca837bc35fe5647de6aa95989652a5a9648dc/tools/ngsderive.wdl/#L80"
 
 [[diagnostics]]
@@ -1382,7 +1382,7 @@ permalink = "https://github.com/stjudecloud/workflows/blob/efdca837bc35fe5647de6
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/tools/picard.wdl"
-message = "picard.wdl:982:9: warning[NonmatchingOutput]: output `interval_lists_scatter` is missing from `meta` section in task `scatter_interval_list`"
+message = "picard.wdl:982:9: warning[NonmatchingOutput]: output `interval_lists_scatter` is missing from `meta.outputs` section in task `scatter_interval_list`"
 permalink = "https://github.com/stjudecloud/workflows/blob/efdca837bc35fe5647de6aa95989652a5a9648dc/tools/picard.wdl/#L982"
 
 [[diagnostics]]
@@ -1402,12 +1402,12 @@ permalink = "https://github.com/stjudecloud/workflows/blob/efdca837bc35fe5647de6
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/tools/sambamba.wdl"
-message = "sambamba.wdl:219:9: warning[NonmatchingOutput]: output `duplicate_marked_bam_index` is missing from `meta` section in task `markdup`"
+message = "sambamba.wdl:219:9: warning[NonmatchingOutput]: output `duplicate_marked_bam_index` is missing from `meta.outputs` section in task `markdup`"
 permalink = "https://github.com/stjudecloud/workflows/blob/efdca837bc35fe5647de6aa95989652a5a9648dc/tools/sambamba.wdl/#L219"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/tools/sambamba.wdl"
-message = "sambamba.wdl:220:9: warning[NonmatchingOutput]: output `markdup_log` is missing from `meta` section in task `markdup`"
+message = "sambamba.wdl:220:9: warning[NonmatchingOutput]: output `markdup_log` is missing from `meta.outputs` section in task `markdup`"
 permalink = "https://github.com/stjudecloud/workflows/blob/efdca837bc35fe5647de6aa95989652a5a9648dc/tools/sambamba.wdl/#L220"
 
 [[diagnostics]]
@@ -1462,7 +1462,7 @@ permalink = "https://github.com/stjudecloud/workflows/blob/efdca837bc35fe5647de6
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/tools/util.wdl"
-message = "util.wdl:136:9: warning[NonmatchingOutput]: output `split_strings` is missing from `meta` section in task `split_string`"
+message = "util.wdl:136:9: warning[NonmatchingOutput]: output `split_strings` is missing from `meta.outputs` section in task `split_string`"
 permalink = "https://github.com/stjudecloud/workflows/blob/efdca837bc35fe5647de6aa95989652a5a9648dc/tools/util.wdl/#L136"
 
 [[diagnostics]]
@@ -1642,12 +1642,12 @@ permalink = "https://github.com/stjudecloud/workflows/blob/efdca837bc35fe5647de6
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/workflows/qc/quality-check-standard.wdl"
-message = "quality-check-standard.wdl:453:9: warning[NonmatchingOutput]: output `inferred_endedness` is missing from `meta` section in workflow `quality_check`"
+message = "quality-check-standard.wdl:453:9: warning[NonmatchingOutput]: output `inferred_endedness` is missing from `meta.outputs` section in workflow `quality_check`"
 permalink = "https://github.com/stjudecloud/workflows/blob/efdca837bc35fe5647de6aa95989652a5a9648dc/workflows/qc/quality-check-standard.wdl/#L453"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/workflows/qc/quality-check-standard.wdl"
-message = "quality-check-standard.wdl:492:9: warning[NonmatchingOutput]: output `intermediate_files` is missing from `meta` section in workflow `quality_check`"
+message = "quality-check-standard.wdl:492:9: warning[NonmatchingOutput]: output `intermediate_files` is missing from `meta.outputs` section in workflow `quality_check`"
 permalink = "https://github.com/stjudecloud/workflows/blob/efdca837bc35fe5647de6aa95989652a5a9648dc/workflows/qc/quality-check-standard.wdl/#L492"
 
 [[diagnostics]]

Gauntlet.toml

@@ -24,11 +24,11 @@ commit_hash = "4e7fdfa7992dd1bf4c4721e77c81e4d7b8ecf4fe"
 
 [repositories."broadinstitute/warp"]
 identifier = "broadinstitute/warp"
-commit_hash = "e52f2c1aabdb88b565c132e5587d05b91c4e6c0f"
+commit_hash = "b8a753edd8e761a835164cc7b84f136c7fbe51d1"
 
 [repositories."chanzuckerberg/czid-workflows"]
 identifier = "chanzuckerberg/czid-workflows"
-commit_hash = "b7c97a87d995a31d85bb6c8ee780fdf33d5bc176"
+commit_hash = "ee513b4b7a79c5a8fe359c6bf6a6b15db33591ab"
 
 [repositories."getwilds/ww-fastq-to-cram"]
 identifier = "getwilds/ww-fastq-to-cram"
@@ -49,7 +49,7 @@ filters = ["/template/task-templates.wdl"]
 
 [repositories."theiagen/public_health_bioinformatics"]
 identifier = "theiagen/public_health_bioinformatics"
-commit_hash = "59ee38708ffdfc5dbbdd2f0df3ab02064570447a"
+commit_hash = "23552eaa4e151bc34745af3b90ff7b13154addd1"
 
 [[diagnostics]]
 document = "aws-samples/amazon-omics-tutorials:/example-workflows/gatk-best-practices/workflows/somatic-snps-and-indels/mutec2.wdl"
@@ -384,34 +384,34 @@ permalink = "https://github.com/broadinstitute/palantir-workflows/blob/4e7fdfa79
 [[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/e52f2c1aabdb88b565c132e5587d05b91c4e6c0f/pipelines/skylab/scATAC/scATAC.wdl/#L203"
+permalink = "https://github.com/broadinstitute/warp/blob/b8a753edd8e761a835164cc7b84f136c7fbe51d1/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/e52f2c1aabdb88b565c132e5587d05b91c4e6c0f/tasks/broad/GermlineVariantDiscovery.wdl/#L137"
+permalink = "https://github.com/broadinstitute/warp/blob/b8a753edd8e761a835164cc7b84f136c7fbe51d1/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/e52f2c1aabdb88b565c132e5587d05b91c4e6c0f/tasks/broad/GermlineVariantDiscovery.wdl/#L65"
+permalink = "https://github.com/broadinstitute/warp/blob/b8a753edd8e761a835164cc7b84f136c7fbe51d1/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/e52f2c1aabdb88b565c132e5587d05b91c4e6c0f/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl/#L814"
+permalink = "https://github.com/broadinstitute/warp/blob/b8a753edd8e761a835164cc7b84f136c7fbe51d1/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/e52f2c1aabdb88b565c132e5587d05b91c4e6c0f/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl/#L866"
+permalink = "https://github.com/broadinstitute/warp/blob/b8a753edd8e761a835164cc7b84f136c7fbe51d1/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/e52f2c1aabdb88b565c132e5587d05b91c4e6c0f/tests/cemba/pr/CheckCembaOutputs.wdl/#L1"
+permalink = "https://github.com/broadinstitute/warp/blob/b8a753edd8e761a835164cc7b84f136c7fbe51d1/tests/cemba/pr/CheckCembaOutputs.wdl/#L1"
 
 [[diagnostics]]
 document = "chanzuckerberg/czid-workflows:/workflows/index-generation/index-generation.wdl"
 message = "index-generation.wdl:1:9: error: unsupported WDL version `development`"
-permalink = "https://github.com/chanzuckerberg/czid-workflows/blob/b7c97a87d995a31d85bb6c8ee780fdf33d5bc176/workflows/index-generation/index-generation.wdl/#L1"
+permalink = "https://github.com/chanzuckerberg/czid-workflows/blob/ee513b4b7a79c5a8fe359c6bf6a6b15db33591ab/workflows/index-generation/index-generation.wdl/#L1"

wdl-ast/src/v1/task.rs

@@ -580,7 +580,7 @@ impl AstNode for MetadataSection {
 
 /// Represents a metadata object item.
 #[derive(Clone, Debug, PartialEq, Eq)]
-pub struct MetadataObjectItem(SyntaxNode);
+pub struct MetadataObjectItem(pub(crate) SyntaxNode);
 
 impl MetadataObjectItem {
     /// Gets the name of the item.

wdl-ast/src/validation.rs

@@ -272,6 +272,17 @@ impl Visitor for Validator {
         }
     }
 
+    fn metadata_object_item(
+        &mut self,
+        state: &mut Self::State,
+        reason: VisitReason,
+        item: &v1::MetadataObjectItem,
+    ) {
+        for visitor in self.visitors.iter_mut() {
+            visitor.metadata_object_item(state, reason, item);
+        }
+    }
+
     fn unbound_decl(
         &mut self,
         state: &mut Self::State,

wdl-ast/src/visitor.rs

@@ -32,6 +32,7 @@ use crate::v1::Expr;
 use crate::v1::ImportStatement;
 use crate::v1::InputSection;
 use crate::v1::MetadataObject;
+use crate::v1::MetadataObjectItem;
 use crate::v1::MetadataSection;
 use crate::v1::OutputSection;
 use crate::v1::ParameterMetadataSection;
@@ -185,6 +186,15 @@ pub trait Visitor: Send + Sync {
     ) {
     }
 
+    /// Visits a metadata object item in a metadata object.
+    fn metadata_object_item(
+        &mut self,
+        state: &mut Self::State,
+        reason: VisitReason,
+        item: &MetadataObjectItem,
+    ) {
+    }
+
     /// Visits an unbound declaration node.
     fn unbound_decl(&mut self, state: &mut Self::State, reason: VisitReason, decl: &UnboundDecl) {}
 
@@ -314,9 +324,13 @@ pub(crate) fn visit<V: Visitor>(root: &SyntaxNode, state: &mut V::State, visitor
                 reason,
                 &MetadataObject(element.into_node().unwrap()),
             ),
-            SyntaxKind::MetadataObjectItemNode
-            | SyntaxKind::MetadataArrayNode
-            | SyntaxKind::LiteralNullNode => {
+            SyntaxKind::MetadataObjectItemNode => visitor.metadata_object_item(
+                state,
+                reason,
+                &MetadataObjectItem(element.into_node().unwrap()),
+            ),
+
+            SyntaxKind::MetadataArrayNode | SyntaxKind::LiteralNullNode => {
                 // Skip these nodes as they're part of a metadata section
             }
             k if Expr::can_cast(k) => visitor.expr(

wdl-lint/src/lib.rs

@@ -92,7 +92,7 @@ pub fn rules() -> Vec<Box<dyn Rule>> {
         Box::new(rules::SectionOrderingRule),
         Box::new(rules::DeprecatedObjectRule),
         Box::new(rules::DescriptionMissingRule),
-        Box::new(rules::NonmatchingOutputRule),
+        Box::new(rules::NonmatchingOutputRule::default()),
     ];
 
     // Ensure all the rule ids are unique and pascal case