Make WDLOutputJob collect all task outputs (#4602)

Co-authored-by: Adam Novak <anovak@soe.ucsc.edu>

src/toil/wdl/wdltoil.py

@@ -2284,9 +2284,10 @@ def run(self, file_store: AbstractFileStore) -> Promised[WDLBindings]:
         # Make jobs to run all the parts of the workflow
         sink = self.create_subgraph(self._workflow.body, [], bindings)
 
-        if self._workflow.outputs:
+        if self._workflow.outputs != []:  # Compare against empty list as None means there should be outputs
+            # Either the output section is declared and nonempty or it is not declared
             # Add evaluating the outputs after the sink
-            outputs_job = WDLOutputsJob(self._workflow.outputs, sink.rv(), self._execution_dir)
+            outputs_job = WDLOutputsJob(self._workflow, sink.rv(), self._execution_dir)
             sink.addFollowOn(outputs_job)
             # Caller is responsible for making sure namespaces are applied
             self.defer_postprocessing(outputs_job)
@@ -2301,31 +2302,44 @@ class WDLOutputsJob(WDLBaseJob):
 
     Returns an environment with just the outputs bound, in no namespace.
     """
-
-    def __init__(self, outputs: List[WDL.Tree.Decl], bindings: Promised[WDLBindings], execution_dir: Optional[str] = None, **kwargs: Any):
+    def __init__(self, workflow: WDL.Tree.Workflow, bindings: Promised[WDLBindings], execution_dir: Optional[str] = None, **kwargs: Any):
         """
         Make a new WDLWorkflowOutputsJob for the given workflow, with the given set of bindings after its body runs.
         """
         super().__init__(execution_dir, **kwargs)
 
-        self._outputs = outputs
         self._bindings = bindings
+        self._workflow = workflow
 
     def run(self, file_store: AbstractFileStore) -> WDLBindings:
         """
         Make bindings for the outputs.
         """
         super().run(file_store)
 
-        # Evaluate all the outputs in the normal, non-task-outputs library context
-        standard_library = ToilWDLStdLibBase(file_store, self._execution_dir)
-        # Combine the bindings from the previous job
-
-        output_bindings = evaluate_output_decls(self._outputs, unwrap(self._bindings), standard_library)
-
+        if self._workflow.outputs is None:
+            # The output section is not declared
+            # So get all task outputs and return that
+            # First get all task output names
+            output_set = set()
+            for call in self._workflow.body:
+                if isinstance(call, WDL.Tree.Call):
+                    for type_binding in call.effective_outputs:
+                        output_set.add(type_binding.name)
+            # Collect all bindings that are task outputs
+            output_bindings: WDL.Env.Bindings[WDL.Value.Base] = WDL.Env.Bindings()
+            for binding in unwrap(self._bindings):
+                if binding.name in output_set:
+                    # The bindings will already be namespaced with the task namespaces
+                    output_bindings = output_bindings.bind(binding.name, binding.value)
+        else:
+            # Output section is declared and is nonempty, so evaluate normally
+            # Evaluate all the outputs in the normal, non-task-outputs library context
+            standard_library = ToilWDLStdLibBase(file_store, self._execution_dir)
+            # Combine the bindings from the previous job
+            output_bindings = evaluate_output_decls(self._workflow.outputs, unwrap(self._bindings), standard_library)
         return self.postprocess(output_bindings)
 
-
 class WDLRootJob(WDLSectionJob):
     """
     Job that evaluates an entire WDL workflow, and returns the workflow outputs