Rework functions in trajectories processing;fix typos;fix filenames

command_line/cadbiom_cmd/solution_repr.py

@@ -366,12 +366,11 @@ def parse_condition(condition, all_nodes, inhibitors_nodes):
 #    print(dir(ret))
 
 
-def build_graph(i, sol, steps, transitions):
+def build_graph(solution, steps, transitions):
     """Build a graph for the given solution.
 
         - Get & make all needed edges
-        - Draw graph
-        - Save graph in svg/graphml
+        - Build graph
 
     :param arg1: Frontier places.
     :param arg2: List of steps (with events in each step).
@@ -380,6 +379,13 @@ def build_graph(i, sol, steps, transitions):
     :type arg1: <str>
     :type arg2: <list <list>>
     :type arg3: <dict <list <tuple <str>, <str>, <dict <str>: <str>>>>
+    :return:
+        - Networkx graph object.
+        - Nodes corresponding to transitions with conditions.
+        - All nodes in the model
+        - Edges between transition node and nodes in condition
+        - Normal transitions without condition
+    :rtype: <networkx.classes.digraph.DiGraph>, <list>, <list>, <list>, <list>
     """
 
     def filter_transitions(step_event):
@@ -478,7 +484,7 @@ def build_graph(i, sol, steps, transitions):
 
 
     # Get & make all needed edges ##############################################
-    LOGGER.info("BUILD GRAPH FOR SOL: " + str(sol))
+    LOGGER.info("BUILD GRAPH FOR SOL: " + str(solution))
     LOGGER.debug("STEPS: " + str(steps))
 #
 #    print(transitions['_h_2755'])
@@ -487,7 +493,7 @@ def build_graph(i, sol, steps, transitions):
 #    print(transitions['_h_3426'])
 #    exit()
 
-    frontier_places  = sol.split(' ')
+    frontier_places  = solution.split(' ')
     edges_with_cond  = list() # Edges between ori <-> transition node <-> ext
     edges_in_cond    = list() # Edges between transition node and nodes in condition
     transition_nodes = list() # Nodes inserted because of condition in transition
@@ -525,6 +531,35 @@ def build_graph(i, sol, steps, transitions):
     G.add_edges_from(edges_with_cond)
     G.add_edges_from(edges_in_cond)
 
+    return G, transition_nodes, all_nodes, edges_in_cond, edges
+
+
+def draw_graph(solution, solution_index, G,
+               transition_nodes, all_nodes,
+               edges_in_cond, edges):
+    """Draw graph with colors and export it to graphml format.
+
+    .. note:: Legend:
+        - red: frontier places (in solution variable),
+        - white: middle edges,
+        - blue: transition edges
+
+    :param arg1: Solution string (mostly a set of frontier places).
+    :param arg2: Index of the solution in the Cadbiom result file
+        (used to distinguish exported filenames).
+    :param arg3: Networkx graph object.
+    :param arg4: Nodes corresponding to transitions with conditions.
+    :param arg5: All nodes in the model
+    :param arg6: Edges between transition node and nodes in condition
+    :param arg7: Normal transitions without condition
+    :type arg1: <str>
+    :type arg2: <int>
+    :type arg3: <networkx.classes.digraph.DiGraph>
+    :type arg4: <list>
+    :type arg5: <list>
+    :type arg6: <list>
+    :type arg7: <list>
+    """
 
     # Drawing ##################################################################
     # draw_circular(G, **kwargs) On a circle.
@@ -550,6 +585,7 @@ def build_graph(i, sol, steps, transitions):
     # - red: frontier places (in solution variable),
     # - white: middle edges,
     # - blue: transition edges
+    frontier_places  = set(solution.split(' '))
     def color_map(node):
         # print("color for:", node)
         if node in frontier_places: # Test first (see cond below)
@@ -578,26 +614,26 @@ def build_graph(i, sol, steps, transitions):
     edges_labels = {(edge[0], edge[1]): edge[2]['label'] for edge in edges}
     nx.draw_networkx_edge_labels(G, pos, edges_labels, label_pos=0.3)
 
-
     # Save & show
-    date = dt.datetime.now().strftime("%H-%M-%S-%f")
+    date = dt.datetime.now().strftime("%H-%M-%S")
     plt.legend()
 #    plt.savefig(GRAPHS_DIR + date + '_' + sol[:75] + ".svg", format="svg")
 #    plt.show()
 
     nx.write_graphml(
         G,
-        GRAPHS_DIR + date + '_' + str(i) +'_' + sol[:75] + ".graphml"
+        "{}{}_{}_{}.graphml".format(
+            GRAPHS_DIR, date, solution_index, solution[:75]
+        )
     )
-    #nx.write_gml(G, date + '_' + sol + ".gml")
 
 
 def process_solutions(sol_steps, transitions):
     """Build a graph per solution"""
 
-    for i, (sol, steps) in enumerate(sol_steps):
+    for sol_index, (sol, steps) in enumerate(sol_steps):
 
-        build_graph(i, sol, steps, transitions)
+        draw_graph(sol, sol_index, *build_graph(sol, steps, transitions))
 
 
 def test_main():