flake8

Author: antgonza

qiita_pet/handlers/software.py

@@ -74,6 +74,7 @@ def _default_parameters_parsing(node):
         # for easy look up and merge of output_names
         main_nodes = dict()
         not_used_nodes = {n.id: n for n in graph.nodes}
+        standalone_input = None
         for i, (x, y) in enumerate(graph.edges):
             if x.id in not_used_nodes:
                 del not_used_nodes[x.id]
@@ -89,10 +90,16 @@ def _default_parameters_parsing(node):
             if i == 0:
                 # we are in the first element so we can specifically select
                 # the type we are looking for
-                if at in input_x[0][1]:
+                if input_x and at in input_x[0][1]:
                     input_x[0][1] = at
-                else:
+                elif input_x:
                     input_x[0][1] = '** WARNING, NOT DEFINED **'
+                else:
+                    # if we get to this point it means that the workflow has a
+                    # multiple commands starting from the main single input,
+                    # thus is fine to link them to the same raw data
+                    standalone_input = vals_x[0]
+                    input_x = [['', at]]
 
             name_x = vals_x[0]
             name_y = vals_y[0]
@@ -106,6 +113,8 @@ def _default_parameters_parsing(node):
                         name = inputs[b]
                     else:
                         name = 'input_%s_%s' % (name_x, b)
+                        if standalone_input is not None:
+                            standalone_input = name
                     vals = [name, a, b]
                     if vals not in nodes:
                         inputs[b] = name
@@ -152,13 +161,12 @@ def _default_parameters_parsing(node):
         # adding nodes without edges
         # as a first step if not_used_nodes is not empty we'll confirm that
         # nodes/edges are empty; in theory we should never hit this
-        if not_used_nodes and (nodes or edges):
+        if not_used_nodes and (nodes or edges) and standalone_input is None:
             raise ValueError(
                 'Error, please check your workflow configuration')
 
         # note that this block is similar but not identical to adding connected
         # nodes
-        standalone_input = None
         for i, (_, x) in enumerate(not_used_nodes.items()):
             vals_x, input_x, output_x = _default_parameters_parsing(x)
             if input_x and at in input_x[0][1]:
@@ -181,8 +189,8 @@ def _default_parameters_parsing(node):
                     else:
                         name = 'input_%s_%s' % (name_x, b)
                     # if standalone_input == name_x then this is the first time
-                    # we are adding an standalone command and we need to add the node
-                    # (only once) and store the name of the node for future usage
+                    # we are processing a standalone command so we need to add
+                    # the node and store the name of the node for future usage
                     if standalone_input == name_x:
                         nodes.append([name, a, b])
                         standalone_input = name