ensure optional fields in structs from input JSON

Populate optional fields with None values when the input JSON omits them. This was done for `read_json()`, but not the case where the struct is read from a runner input JSON file.

#686

.github/workflows/CI.yml

@@ -16,6 +16,14 @@ jobs:
           # - skylab_bulk_rna
     runs-on: ubuntu-20.04
     steps:
+    - name: Maximize build space
+      uses: AdityaGarg8/remove-unwanted-software@v3
+      with:
+        remove-dotnet: 'true'
+        remove-android: 'true'
+        remove-haskell: 'true'
+        remove-codeql: 'true'
+      if: ${{ matrix.ci_target == 'viral_assemble' }}
     - name: Login to GitHub Packages Docker Registry
       uses: docker/login-action@v1
       with:

WDL/Expr.py

@@ -942,7 +942,8 @@ class Get(Base):
 
     def __init__(self, pos: SourcePosition, expr: Base, member: Optional[str]) -> None:
         super().__init__(pos)
-        assert expr
+        assert isinstance(expr, Base)
+        assert isinstance(member, (str, type(None)))
         self.expr = expr
         self.member = member
 

WDL/Value.py

@@ -579,7 +579,8 @@ def from_json(type: Type.Base, value: Any) -> Base:
                     raise Error.InputError(
                         f"couldn't initialize struct {str(type)} {type.members[k]} {k} from {json.dumps(v)}"
                     ) from None
-        return Struct(Type.Object(type.members), items, extra=extra)
+        # Struct.__init__ will populate null for any omitted optional members
+        return Struct(type, items, extra=extra)
     if type.optional and value is None:
         return Null()
     raise Error.InputError(f"couldn't construct {str(type)} from {json.dumps(value)}")

WDL/_parser.py

@@ -257,8 +257,10 @@ def left_name(self, meta, items) -> Expr.Base:
         return Expr.Get(self._sp(meta), Expr._LeftName(self._sp(meta), items[0]), None)
 
     def get_name(self, meta, items) -> Expr.Base:
-        assert len(items) == 2 and isinstance(items[0], Expr.Base) and isinstance(items[1], str)
-        return Expr.Get(self._sp(meta), items[0], items[1])
+        assert (
+            len(items) == 2 and isinstance(items[0], Expr.Base) and isinstance(items[1].value, str)
+        )
+        return Expr.Get(self._sp(meta), items[0], items[1].value)
 
 
 # _ExprTransformer infix operators

tests/runner.t

@@ -11,7 +11,7 @@ source tests/bash-tap/bash-tap-bootstrap
 export PYTHONPATH="$SOURCE_DIR:$PYTHONPATH"
 miniwdl="python3 -m WDL"
 
-plan tests 89
+plan tests 90
 
 $miniwdl run_self_test
 is "$?" "0" "run_self_test"
@@ -599,3 +599,31 @@ workflow outer {
 EOF
 MINIWDL__SCHEDULER__SUBWORKFLOW_CONCURRENCY=2 $miniwdl run --dir nested_deadlock outer.wdl
 is "$?" "0" "avoid deadlocking on nested subworkflows"
+
+cat << 'EOF' > issue686.wdl
+version 1.1
+
+struct ReadGroup {
+    String ID
+    String? KS
+}
+
+task test_task {
+    input {
+        ReadGroup read_group
+    }
+
+    command <<<
+        if [ -z "~{read_group.KS}" ]
+        then
+            echo "KS is empty"
+        fi
+    >>>
+}
+EOF
+$miniwdl run issue686.wdl -i '{
+    "read_group": {
+        "ID": "test"
+    }
+}'
+is "$?" "0" "ensure optional fields in structs initialized from JSON (issue 686 regression)"