fixing graph performance issue (invoking @Property only once)

isatools/isatab.py

@@ -1179,23 +1179,24 @@ def write_study_table_files(inv_obj, output_dir):
     if not isinstance(inv_obj, Investigation):
         raise NotImplementedError
     for study_obj in inv_obj.studies:
-        if study_obj.graph is None:
+        s_graph = study_obj.graph
+        if s_graph is None:
             break
         protrefcount = 0
         protnames = dict()
 
         def flatten(l): return [item for sublist in l for item in sublist]
         columns = []
 
-        # start_nodes, end_nodes = _get_start_end_nodes(study_obj.graph)
+        # start_nodes, end_nodes = _get_start_end_nodes(s_graph)
         paths = _all_end_to_end_paths(
-            study_obj.graph,
-            [x for x in study_obj.graph.nodes() if isinstance(study_obj.graph.indexes[x], Source)])
-        log.warning(study_obj.graph.nodes())
+            s_graph,
+            [x for x in s_graph.nodes() if isinstance(s_graph.indexes[x], Source)])
+        log.warning(s_graph.nodes())
         sample_in_path_count = 0
-        longest_path = _longest_path_and_attrs(paths, study_obj.graph.indexes)
+        longest_path = _longest_path_and_attrs(paths, s_graph.indexes)
         for node_index in longest_path:
-            node = study_obj.graph.indexes[node_index]
+            node = s_graph.indexes[node_index]
             if isinstance(node, Source):
                 olabel = "Source Name"
                 columns.append(olabel)
@@ -1252,7 +1253,7 @@ def pbar(x): return x"""
 
             sample_in_path_count = 0
             for node_index in path:
-                node = study_obj.graph.indexes[node_index]
+                node = s_graph.indexes[node_index]
                 if isinstance(node, Source):
                     olabel = "Source Name"
                     df_dict[olabel][-1] = node.name
@@ -1376,26 +1377,27 @@ def write_assay_table_files(inv_obj, output_dir, write_factor_values=False):
     protocol_types_dict = load_protocol_types_info()
     for study_obj in inv_obj.studies:
         for assay_obj in study_obj.assays:
-            if assay_obj.graph is None:
+            a_graph = assay_obj.graph
+            if a_graph is None:
                 break
             protrefcount = 0
             protnames = dict()
 
             def flatten(l): return [item for sublist in l for item in sublist]
             columns = []
 
-            # start_nodes, end_nodes = _get_start_end_nodes(assay_obj.graph)
+            # start_nodes, end_nodes = _get_start_end_nodes(a_graph)
             paths = _all_end_to_end_paths(
-                assay_obj.graph, [x for x in assay_obj.graph.nodes()
-                                  if isinstance(assay_obj.graph.indexes[x], Sample)])
+                a_graph, [x for x in a_graph.nodes()
+                                  if isinstance(a_graph.indexes[x], Sample)])
             if len(paths) == 0:
                 log.info("No paths found, skipping writing assay file")
                 continue
-            if _longest_path_and_attrs(paths, assay_obj.graph.indexes) is None:
+            if _longest_path_and_attrs(paths, a_graph.indexes) is None:
                 raise IOError(
                     "Could not find any valid end-to-end paths in assay graph")
-            for node_index in _longest_path_and_attrs(paths, assay_obj.graph.indexes):
-                node = assay_obj.graph.indexes[node_index]
+            for node_index in _longest_path_and_attrs(paths, a_graph.indexes):
+                node = a_graph.indexes[node_index]
                 if isinstance(node, Sample):
                     olabel = "Sample Name"
                     columns.append(olabel)
@@ -1474,7 +1476,7 @@ def pbar(x): return x
                     df_dict[k].extend([""])
 
                 for node_index in path:
-                    node = assay_obj.graph.indexes[node_index]
+                    node = a_graph.indexes[node_index]
                     if isinstance(node, Process):
                         olabel = "Protocol REF.{}".format(
                             node.executes_protocol.name

tests/test_create_connectors.py

@@ -188,6 +188,9 @@ def test_generate_study_design(self):
             separators=(',', ': ')
         )
         self.assertIsInstance(inv_json, str)
+        isatab_txt = isatab.dumps(investigation)
+        print(isatab_txt)
+        self.assertTrue(isatab_txt)
         if SLOW_TESTS:
             data_frames = isatab.dump_tables_to_dataframes(investigation)
             self.assertIsInstance(data_frames, dict)