From 0e9568e083bf8af4f96f77cb09d2c6cb5b3db322 Mon Sep 17 00:00:00 2001
From: Mike Lin <mlin@mlin.net>
Date: Thu, 23 May 2019 22:58:04 -0700
Subject: [PATCH] exclude output declarations from Workflow.available_inputs

---
 WDL/Tree.py        | 12 ++++++++----
 tests/test_1doc.py | 16 ++++++++++++++++
 2 files changed, 24 insertions(+), 4 deletions(-)

diff --git a/WDL/Tree.py b/WDL/Tree.py
index a27ba2e6..ad9f3798 100644
--- a/WDL/Tree.py
+++ b/WDL/Tree.py
@@ -736,7 +736,7 @@ def available_inputs(self) -> Env.Decls:
             for decl in self.inputs:
                 ans = Env.bind(ans, [], decl.name, decl)
 
-        for elt in _decls_and_calls(self):
+        for elt in _decls_and_calls(self, exclude_outputs=True):
             if isinstance(elt, Decl):
                 if self.inputs is None:
                     ans = Env.bind(ans, [], elt.name, elt)
@@ -760,7 +760,7 @@ def required_inputs(self) -> Env.Decls:
                 if decl.expr is None and decl.type.optional is False:
                     ans = Env.bind(ans, [], decl.name, decl)
 
-        for elt in _decls_and_calls(self):
+        for elt in _decls_and_calls(self, exclude_outputs=True):
             if isinstance(elt, Decl):
                 if self.inputs is None and elt.expr is None and elt.type.optional is False:
                     ans = Env.bind(ans, [], elt.name, elt)
@@ -1060,11 +1060,15 @@ def load(
 
 
 def _decls_and_calls(
-    element: Union[Workflow, Scatter, Conditional]
+    element: Union[Workflow, Scatter, Conditional], exclude_outputs: bool = True
 ) -> Generator[Union[Decl, Call], None, None]:
     # Yield each Decl and Call in the workflow, including those nested within
     # scatter/conditional sections
-    for ch in element.children:
+    children = element.children
+    if isinstance(element, Workflow) and exclude_outputs:
+        children = element.inputs if element.inputs else []
+        children = children + element.elements
+    for ch in children:
         if isinstance(ch, (Decl, Call)):
             yield ch
         elif isinstance(ch, (Scatter, Conditional)):
diff --git a/tests/test_1doc.py b/tests/test_1doc.py
index 90872370..08310df6 100644
--- a/tests/test_1doc.py
+++ b/tests/test_1doc.py
@@ -1279,6 +1279,22 @@ def test_multi_errors(self):
         except WDL.Error.MultipleValidationErrors as multi:
             self.assertEqual(len(multi.exceptions), 2)
 
+    def test_issue135_workflow_available_inputs(self):
+        # Workflow.available_inputs should not include declarations in the
+        # output section
+        doc = r"""
+        workflow a {
+            File in
+            output {
+                File out = in
+            }
+        }
+        """
+        doc = WDL.parse_document(doc)
+        doc.typecheck()
+        self.assertEqual(len(doc.workflow.available_inputs), 1)
+        self.assertEqual(doc.workflow.available_inputs[0].name, "in")
+
 class TestCycleDetection(unittest.TestCase):
     def test_task(self):
         doc = r"""