Cython: fixed history dot graph for all views, and fixed history

recording for build_ref_db and ecotag

python/obitools3/commands/build_ref_db.pyx

@@ -75,7 +75,11 @@ def run(config):
 
     # Save command config in View comments
     command_line = " ".join(sys.argv[1:])
-    comments = View.print_config(config, "build_ref_db", command_line, input_dms_name=[i_dms_name], input_view_name=[i_view_name])
+    input_dms_name=[i_dms_name]
+    input_view_name= [i_view_name]
+    input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
+    input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
+    comments = View.print_config(config, "build_ref_db", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
 
     if build_reference_db(tobytes(i_dms_name), tobytes(i_view_name), tobytes(taxonomy_name), tobytes(o_view_name), comments, config['build_ref_db']['threshold']) < 0:
         raise Exception("Error building a reference database")
@@ -96,3 +100,4 @@ def run(config):
         o_dms.close()
     
     i_dms.close()
+

python/obitools3/commands/ecotag.pyx

@@ -93,7 +93,13 @@ def run(config):
 
     # Save command config in View comments
     command_line = " ".join(sys.argv[1:])
-    comments = View.print_config(config, "ecotag", command_line, input_dms_name=[i_dms_name], input_view_name=[i_view_name])  # TODO no. fix
+    input_dms_name=[i_dms_name]
+    input_view_name= [i_view_name]
+    input_dms_name.append(ref_dms_name)
+    input_view_name.append(ref_view_name)
+    input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
+    input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
+    comments = View.print_config(config, "ecotag", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
 
     if obi_ecotag(tobytes(i_dms_name), tobytes(i_view_name), \
                   tobytes(ref_dms_name), tobytes(ref_view_name), \

python/obitools3/dms/view/view.pyx

@@ -485,7 +485,7 @@ cdef class View(OBIWrapper) :
     @property
     def dot_history_graph(self):
         uniq_graph = []
-        for elt in self.history_graph_list:
+        for elt in self.dot_history_graph_list:
             if elt not in uniq_graph:
                 uniq_graph.append(elt)
         uniq_graph.insert(0, b"digraph \""+self.name+b"\" {\n")