#23 test_export_as_gfa now working with example fast queries for fetc…

…hing the whole graph.

Graph/gfa.py

@@ -103,12 +103,16 @@ def save_as_gfa(self, file: str):
         self.gfa.to_file(file)
 
     @classmethod
-    def from_graph(cls, graph: GraphGenome):
+    def from_graph(cls, graph: GraphGenome):  # TODO: should be given ZoomLevel instead
         """Constructs the lines of a GFA file listing paths, then sequence nodes in arbitrary order."""
         gfa = gfapy.Gfa()
-        for path in graph.paths:
-            visits = [traverse.node_name + traverse.strand for traverse in
-                     path.nodes.values_list('node_name', 'strand', named=True)]
+        for path in graph.paths.all():
+            visits = []
+            # example of using lazy queries and values_list for fast lookup
+            node_infos = path.nodes.values_list('node_id', 'strand', named=True)
+            for traverse in node_infos:
+                name = Node.objects.values_list('name', flat=True).get(id=traverse.node_id)  # fast lookup
+                visits.append(name + traverse.strand)
             node_series = ",".join(visits)
             connections = ",".join(['*'] * path.nodes.count())  # count -1?
             gfa.add_line('\t'.join(['P', path.accession, node_series, connections]))

Graph/migrations/0004_ZoomLevel_objects.py

@@ -6,8 +6,6 @@
 
 class Migration(migrations.Migration):
 
-    replaces = [('Graph', '0004_ZoomLevel_objects'), ('Graph', '0005_auto_20190823_1603')]
-
     dependencies = [
         ('Graph', '0003_add_zoom_levels'),
     ]

Graph/test.py

@@ -66,14 +66,15 @@ def test_summary_storage(self):
             current = graph.node(node_name)
             NodeTraversal(node=current, path=path, strand='+', order=i).save()
         assert NodeTraversal.objects.get(order=0, path=path).downstream().downstream().node.name == '6'
-        child = graph.paths.get(accession='a')
-        child.update(summarized_by=path)
         assert graph.zoomlevel_set.count() == 2
+        graph.paths.filter(accession='a').update(summarized_by=path)
+        assert bool(path.summary_child), "Path should be linked to its child."
         path_pointers = graph.zoomlevel_set.filter(zoom=1).first().paths
         print('path_pointers', type(path_pointers))
         assert path_pointers.count() == 1
 
-# @unittest.skip  # DAGify has not been converted to databases yet.
+
+#@unittest.skip  # DAGify has not been converted to databases yet.
 class DAGifyTest(TestCase):
     """ test class of sort.py
     """