Merge c48fef3 into 6d66bf4

.gitmodules

@@ -43,3 +43,6 @@
 [submodule "tests/bash-tap"]
 	path = tests/bash-tap
 	url = https://github.com/illusori/bash-tap.git
+[submodule "test_corpi/biowdl/tasks"]
+	path = test_corpi/biowdl/tasks
+	url = https://github.com/biowdl/tasks.git

WDL/Lint.py

@@ -654,12 +654,12 @@ def decl(self, obj: WDL.Tree.Decl) -> Any:
             if not (
                 (
                     isinstance(obj.type, WDL.Type.File)
-                    and sum(1 for sfx in index_suffixes if obj.name.endswith(sfx))
+                    and sum(1 for sfx in index_suffixes if obj.name.lower().endswith(sfx))
                 )
                 or (
                     isinstance(obj.type, WDL.Type.Array)
                     and isinstance(obj.type.item_type, WDL.Type.File)
-                    and sum(1 for sfx in index_suffixes if obj.name.endswith(sfx))
+                    and sum(1 for sfx in index_suffixes if obj.name.lower().endswith(sfx))
                 )
                 or (
                     isinstance(pt, WDL.Tree.Task)

WDL/Tree.py

@@ -825,6 +825,8 @@ def typecheck(self, doc: TVDocument, check_quant: bool) -> None:
             # 5. typecheck the output expressions
             if self.outputs:
                 output_names = set()
+                output_type_env = self._type_env
+                assert output_type_env
                 for output in self.outputs:
                     assert output.expr
                     if output.name in output_names:
@@ -835,10 +837,11 @@ def typecheck(self, doc: TVDocument, check_quant: bool) -> None:
                         )
                     errors.try1(
                         lambda output=output: output.typecheck(
-                            self._type_env, check_quant=check_quant
+                            output_type_env, check_quant=check_quant
                         )
                     )
                     output_names.add(output.name)
+                    output_type_env = Env.bind(output_type_env, [], output.name, output.type)
         # 6. check for cyclic dependencies
         WDL._util.detect_cycles(_dependency_matrix(_decls_and_calls(self)))  # pyre-fixme
 
@@ -1387,7 +1390,7 @@ def _resolve_struct_typedef(
     try:
         struct_typedef = Env.resolve(struct_typedefs, [], ty.type_name)
     except KeyError:
-        raise Err.InvalidType(pos, "Unknown type " + ty.type_name)
+        raise Err.InvalidType(pos, "Unknown type " + ty.type_name) from None
     ty.members = struct_typedef.members
 
 
@@ -1418,7 +1421,7 @@ def _initialize_struct_typedefs(struct_typedefs: Env.StructTypeDefs):
             try:
                 _resolve_struct_typedefs(b.rhs.pos, member_ty, struct_typedefs)
             except StopIteration:
-                raise Err.CircularDependencies(b.rhs)
+                raise Err.CircularDependencies(b.rhs) from None
 
 
 def _add_struct_instance_to_type_env(

WDL/_parser.py

@@ -61,16 +61,12 @@
 // WDL tasks
 input_decls: "input" "{" any_decl* "}"
 output_decls: "output" "{" bound_decl* "}"
-?task_sections1: input_decls
-               | output_decls
-               | meta_section
-               | runtime_section
-               | any_decl+ -> noninput_decls
-?task_sections2: input_decls
-               | output_decls
-               | meta_section
-               | runtime_section
-task: "task" CNAME "{" task_sections1* command task_sections2* "}"
+?task_section: input_decls
+             | output_decls
+             | meta_section
+             | runtime_section
+             | any_decl -> noninput_decl
+task: "task" CNAME "{" task_section* command task_section* "}"
 
 tasks: task*
 
@@ -262,7 +258,7 @@ def parse(txt: str, start: str, version: Optional[str] = None) -> lark.Tree:
         _lark_cache[(version, start)] = lark.Lark(
             _grammar_for_version(version), start=start, parser="lalr", propagate_positions=True
         )
-    return _lark_cache[(version, start)].parse(txt)
+    return _lark_cache[(version, start)].parse(txt + ("\n" if not txt.endswith("\n") else ""))
 
 
 def sp(filename, meta) -> SourcePosition:
@@ -484,8 +480,8 @@ def decl(self, items, meta):
     def input_decls(self, items, meta):
         return {"inputs": items}
 
-    def noninput_decls(self, items, meta):
-        return {"decls": items}
+    def noninput_decl(self, items, meta):
+        return {"noninput_decl": items[0]}
 
     def placeholder_option(self, items, meta):
         assert len(items) == 2
@@ -547,15 +543,18 @@ def runtime_section(self, items, meta):
         return {"runtime": d}
 
     def task(self, items, meta):
-        d = {}
+        d = {"noninput_decls": []}
         for item in items:
             if isinstance(item, dict):
                 for k, v in item.items():
-                    if k in d:
+                    if k == "noninput_decl":
+                        d["noninput_decls"].append(v)
+                    elif k in d:
                         raise Err.MultipleDefinitions(
                             sp(self.filename, meta), "redundant sections in task"
                         )
-                    d[k] = v
+                    else:
+                        d[k] = v
             else:
                 assert isinstance(item, str)
                 assert "name" not in d
@@ -565,7 +564,7 @@ def task(self, items, meta):
             sp(self.filename, meta),
             d["name"],
             d.get("inputs", None),
-            d.get("decls", []),
+            d["noninput_decls"],
             d["command"],
             d.get("outputs", []),
             d.get("parameter_meta", {}),

tests/test_1doc.py

@@ -1187,7 +1187,9 @@ def test_workflow_inputs(self):
                 y = y
             }
             output {
-                Int z = z
+                Int z = z+1
+                Int w = x+y
+                Array[Int] outs = [z,w]
             }
         }
         """

tests/test_3corpi.py

@@ -200,3 +200,16 @@ class Contrived(unittest.TestCase):
 )
 class Contrived2(unittest.TestCase):
     pass
+
+@test_corpus(
+    ["test_corpi/biowdl/tasks/**"],
+    expected_lint={'OptionalCoercion': 4, 'NonemptyCoercion': 1, 'UnnecessaryQuantifier': 3, 'UnusedDeclaration': 9},
+    check_quant=False,
+    blacklist=[
+        # use Object
+        "common", "bamstats", "seqstat", "flash", "sampleconfig", "strelka",
+        "stringtie", "vardict", "manta", "somaticseq", "biopet",
+    ],
+)
+class BioWDLTasks(unittest.TestCase):
+    pass