more NameCollision cases and tests

WDL/Lint.py

@@ -308,7 +308,12 @@ class NameCollision(Linter):
     # Name collisions between
     # - call and import
     # - call and decl
+    # - call and its containing workflow
     # - decl and import
+    # - decl and workflow
+    # - decl and task
+    # - workflow and import
+    # - task and import
     # These are allowed, but potentially confusing.
     # TODO: cover scatter variables
     def call(self, obj: WDL.Call) -> Any:
@@ -317,12 +322,15 @@ def call(self, obj: WDL.Call) -> Any:
             doc = getattr(doc, "parent")
         for _, namespace, _ in doc.imports:
             if namespace == obj.name:
-                msg = "call name {} collides with imported document namespace".format(obj.name)
+                msg = "call name '{}' collides with imported document namespace".format(obj.name)
                 self.add(obj, msg)
+        if doc.workflow and doc.workflow.name == obj.name:
+            msg = "call name '{}' collides with workflow name".format(obj.name)
+            self.add(obj, msg)
         type_env = getattr(obj, "parent")._type_env
         try:
             WDL.Env.resolve(type_env, [], obj.name)
-            msg = "call name {} collides with declared value".format(obj.name)
+            msg = "call name '{}' collides with declared value".format(obj.name)
             self.add(obj, msg)
         except KeyError:
             pass
@@ -334,8 +342,39 @@ def decl(self, obj: WDL.Decl) -> Any:
             doc = getattr(doc, "parent")
         for _, namespace, _ in doc.imports:
             if namespace == obj.name:
-                msg = "declaration of {} collides with imported document namespace".format(obj.name)
+                msg = "declaration of '{}' collides with imported document namespace".format(
+                    obj.name
+                )
+                self.add(obj, msg)
+        if doc.workflow and doc.workflow.name == obj.name:
+            msg = "declaration of '{}' collides with workflow name".format(obj.name)
+            self.add(obj, msg)
+        for task in doc.tasks:
+            if obj.name == task.name:
+                msg = "declaration of '{}' collides with a task name".format(obj.name)
+                self.add(obj, msg)
+
+    def workflow(self, obj: WDL.Workflow) -> Any:
+        doc = obj
+        while not isinstance(doc, WDL.Document):
+            doc = getattr(doc, "parent")
+        for _, namespace, _ in doc.imports:
+            if namespace == obj.name:
+                msg = "workflow name '{}' collides with imported document namespace".format(
+                    obj.name
+                )
                 self.add(obj, msg)
+        super().workflow(obj)
+
+    def task(self, obj: WDL.Task) -> Any:
+        doc = obj
+        while not isinstance(doc, WDL.Document):
+            doc = getattr(doc, "parent")
+        for _, namespace, _ in doc.imports:
+            if namespace == obj.name:
+                msg = "task name '{}' collides with imported document namespace".format(obj.name)
+                self.add(obj, msg)
+        super().task(obj)
 
 
 @a_linter
@@ -433,3 +472,4 @@ def call(self, obj: WDL.Tree.Call) -> Any:
                 + obj.name
                 + " nor are are they output from the workflow",
             )
+        super().call(obj)

test_corpi/contrived/contrived.wdl

@@ -1,25 +1,28 @@
-# examples contrived to cover obscured Linter code paths otherwise missed
+# examples contrived to cover obscure Linter code paths otherwise missed
 version 1.0
 
 import "empty.wdl" as popular
+import "empty.wdl" as contrived
 
 workflow contrived {
     String popular = "fox"
-    call echo as popular { input:
+    Int contrived = 42
+    call popular { input:
         popular = popular,
-        i = 42
+        i = contrived,
+        y = contrived
     }
 }
 
-task echo {
+task popular {
     String popular
     String? opt
     Float? i
     String x = popular + opt
-    String y = popular + i
+    Array[String]+ y = select_all([popular + i])
 
     command {
         echo "~{popular}"
-        echo "${x} ${y}"
+        echo "${x} ${sep=';' y}"
     }
 }

tests/test_3corpi.py

@@ -99,7 +99,7 @@ class broad_prod_wgs(unittest.TestCase):
     ["test_corpi/broadinstitute/gtex-pipeline/**"],
     # need URI import
     blacklist=["rnaseq_pipeline_bam","rnaseq_pipeline_fastq"],
-    expected_lint={'IncompleteCall': 30, 'UnusedDeclaration': 3}
+    expected_lint={'IncompleteCall': 30, 'UnusedDeclaration': 3, 'NameCollision': 4},
 )
 class GTEx(unittest.TestCase):
     pass
@@ -117,14 +117,14 @@ class TOPMed(unittest.TestCase):
 @test_corpus(
     ["test_corpi/broadinstitute/viral-ngs/pipes/WDL/workflows"],
     path=[["test_corpi/broadinstitute/viral-ngs/pipes/WDL/workflows/tasks"]],
-    expected_lint={'UnusedDeclaration': 23, 'IncompleteCall': 44, 'UnusedImport': 1}
+    expected_lint={'UnusedDeclaration': 23, 'NameCollision': 9, 'IncompleteCall': 44, 'UnusedImport': 1},
 )
 class ViralNGS(unittest.TestCase):
     pass
 
 @test_corpus(
      ["test_corpi/ENCODE-DCC/chip-seq-pipeline2/**"],
-     expected_lint={'StringCoercion': 192, 'ArrayCoercion': 64, 'OptionalCoercion': 64}
+     expected_lint={'StringCoercion': 192, 'NameCollision': 16, 'ArrayCoercion': 64, 'OptionalCoercion': 64},
 )
 class ENCODE_ChIPseq(unittest.TestCase):
     pass
@@ -162,14 +162,14 @@ class ENCODE_WGBS(unittest.TestCase):
         # double quantifier
         "conditionals_base"
     ],
-    expected_lint={'UnusedDeclaration': 20, 'UnusedCall': 15}
+    expected_lint={'UnusedDeclaration': 20, 'UnusedCall': 15, 'NameCollision': 2}
 )
 class dxWDL(unittest.TestCase):
     pass
 
 @test_corpus(
     ["test_corpi/contrived/**"],
-    expected_lint= {'UnusedImport': 1, 'NameCollision': 4, 'OptionalCoercion': 2, 'StringCoercion': 1},
+    expected_lint={'UnusedImport': 2, 'NameCollision': 10, 'OptionalCoercion': 2, 'StringCoercion': 1, 'NonemptyArrayCoercion': 1, 'ArrayCoercion': 1},
 )
 class Contrived(unittest.TestCase):
     pass