Fix the duplicate outs bug

Author: Vasu Jaganath

src/sophios/api/http/restapi.py

@@ -161,14 +161,6 @@ async def compile_wf(request: Request) -> Json:
 
     cwl_tree_run.pop('steps', None)
     cwl_tree_run['steps'] = cwl_tree_run.pop('steps_dict', None)
-
-    # currently there is a compiler bug where the output variables are duplicated
-    # this is a workaround to remove the duplicates till the compiler is fixed
-    for step in cwl_tree_run['steps']:
-
-        out_vars = cwl_tree_run['steps'][step]['out']
-        out_vars_unique = list(set(out_vars))
-        cwl_tree_run['steps'][step]['out'] = out_vars_unique
     compute_workflow: Json = {}
     compute_workflow = {
         "name": yaml_stem,

src/sophios/api/pythonapi.py

@@ -782,13 +782,6 @@ def get_cwl_workflow(self, args_dict: Dict[str, str] = {}) -> Json:
         sub_node_data = rose_tree.data
         cwl_ast = sub_node_data.compiled_cwl
 
-        # Copy samee's workaround for duplicate outs
-        for step in cwl_ast['steps']:
-            out_vars = step['out']
-            out_vars_unique = list(set(out_vars))
-            out_vars_unique.sort()
-            step['out'] = out_vars_unique
-
         yaml_inputs = sub_node_data.workflow_inputs_file
         workflow_json: Json = {}
         workflow_json = {

src/sophios/utils_cwl.py

@@ -92,6 +92,7 @@ def add_yamldict_keyval_out(steps_i: Yaml, step_key: str, strs: List[str]) -> Ya
     if steps_i:
         if 'out' in steps_i:
             new_strs = steps_i['out'] + strs
+            new_strs = list(set(new_strs))
             new_keyvals = dict([(k, v) if k != 'out' else (k, new_strs) for k, v in steps_i.items()])
         else:
             new_keyvals = dict(list(steps_i.items()) + [('out', strs)])

tests/test_scattering_scaling.py

@@ -13,7 +13,7 @@
 def test_scattering_scaling(minval: int = 100, maxval: int = 500, step: int = 100) -> None:
     """Tests that execution time scales linearly with input array size"""
     # First compile the workflow
-    cmd = ['sophios', '--yaml', 'examples/scattering_scaling.wic']
+    cmd = ['sophios', '--yaml', 'examples/scattering_scaling.wic', '--generate_run_script']
     sub.run(cmd, check=True)
 
     basedir = 'autogenerated'